chore: vendor @joan/procedural-glyph-engine for portable builds

Move @joan/procedural-glyph-engine from absolute path dep
(/private/tmp/orby-pkg) to vendored local dep (web/vendor/) so the
SPA builds in Docker and on other machines without the temp dir.

- Vendor Orby v5.0.0 into web/vendor/
- Switch package.json dep to file:../vendor
- Update Dockerfile to COPY vendor into build context
- Use npm install instead of npm ci (file: deps need install)
- Fix missing trailing newline in Dockerfile

.agents/NOMOS.md

@@ -13,13 +13,13 @@ service itself.
 
 ## Source of truth
 
-The homelab-context repo at `/opt/homelab-context/` is the single source of
+The homelab-context repo at `/opt/homelab/` is the single source of
 truth for:
 - Fleet topology (`inventory.yaml`)
 - Agent behaviour and conventions
 - Everything in this file
 
-When in doubt, check `/opt/homelab-context/` first, or query the Oikos API/MCP
+When in doubt, check `/opt/homelab/` first, or query the Oikos API/MCP
 server directly (see [AGENTS.md](../AGENTS.md) §3-4) — the database is
 authoritative at runtime.
 

.agents/OIKOS.md

@@ -1,8 +1,8 @@
 # Oikos — the operating model
 
 Oikos (Greek: *household*) is the agent operating system layered on this
-repo. It is not new infrastructure: `inventory.yaml` is the kernel data
-structure, the `homelab` CLI and MCP server are the syscall surface, and
+repo. It is not new infrastructure: `seeds/inventory.yaml` is the kernel data
+structure, the Oikos REST API and MCP server are the syscall surface, and
 this page defines the rules everything above them follows.
 
 Read this after [AGENTS.md](../AGENTS.md). Machine-readable companions:
@@ -100,16 +100,16 @@ via the API's `/api/v1/graph` endpoint, and the Mermaid export at
 
 The Oikos runtime was rewritten from Python to Go over 6 phases and is deployed
 in Docker on mac-mini. See
-[plans/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md](../plans/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md)
+[plans/done/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md](../plans/done/2026-07-06-consolidate-oikos-control-plane-onto-mac-mini.md)
 for the full plan. The Python codebase has been removed; all functionality runs
 in the Go binary.
 
 **Phase 1 — Ontology + DB (DONE):**
-- `migrations/` (001–011): TimescaleDB hypertables, entity_status, CAGGs,
-  retention policies, knowledge entities with FTS. Forward-only, idempotent.
+- `migrations/` (001–020, forward-only): TimescaleDB hypertables, entity_status, CAGGs,
+  retention policies, knowledge entities with FTS. Idempotent.
 - `seeds/{ontology,inventory,policy,knowledge}.yaml`: DB-native bootstrap +
-  DR export. Knowledge seed contains 36 documents, 6 investigations, and 12
-  runbooks.
+  DR export. Knowledge seed contents are not hardcoded here — count them
+  from the seed or query the DB.
 - `blast_radius()` SQL CTE, type hierarchy, abstract types, relationship
   validation.
 - Go packages: `internal/db/`, `internal/ontology/`, `internal/domain/`,
@@ -139,8 +139,8 @@ in the Go binary.
 
 **Phase 4 — Agent / Nomos (DONE):**
 - Standalone Nomos MCP client binary (`cmd/nomos`) with gateway mode
-  (:8092). Structured queries + natural-language routing to 15 MCP tools.
-  Agent activity logging on every tool call. No SSH keys.
+  (:8092). Structured queries + natural-language routing to the MCP tool
+  list (see AGENTS.md §3). Agent activity logging on every tool call. No SSH keys.
 - `nomos/` directory with config, SOUL.md, homelab-ops skill.
 - Nomos Docker service in `docker-compose.yml` (profile: full).
 - Go packages: `cmd/nomos/`, `compose/nomos/`.

.agents/dev/CONTRIBUTING.md

@@ -94,7 +94,12 @@ current phase status). To add a new capability:
 ## SQL conventions
 
 - Queries live in `internal/db/queries/*.sql` with `-- name: FuncName :exec`
-  annotations for sqlc
+  annotations for sqlc. Generated code in `internal/db/sqlcgen/` — never
+  hand-edit. Call via `sqlcgen.New(pool).QueryName(ctx, params)`.
+- **sqlc is the default** for all DB access. Raw `pool.Query/Exec` with inline
+  SQL is a documented carve-out for cases sqlc can't express: `LISTEN`/`NOTIFY`,
+  dynamic WHERE-clause builders, `blast_radius()` (opaque return type), and
+  `COPY`. All other DB access should go through sqlc queries.
 - Use `pgx/v5` driver. UUIDs use `pgtype.UUID`, timestamps use `time.Time`
 - CTEs for graph traversals (blast radius, dependency chains)
 - CAGGs and retention policies for TimescaleDB hypertables
@@ -108,6 +113,23 @@ current phase status). To add a new capability:
   implement it in `internal/httpapi/impl.go`
 - Problem+JSON errors via `internal/httpapi/problem.go` — RFC 9457 format
 - Cursor pagination, If-Match/ETag, idempotency keys, SSE streaming
+- **Non-OpenAPI routes carve-out:** ~10 routes are registered manually on
+  the chi router in `internal/httpapi/server.go` rather than generated from
+  `openapi.yaml`. These fall into three categories:
+  1. **Auth/infra** (`/healthz`, `/api/v1/auth/oidc-*`, `/oidc-callback`) —
+     must bypass the auth middleware or aren't JSON API endpoints.
+  2. **SSE override** (`/api/v1/events/stream`) — in the spec but
+     re-registered manually because the strict handler can't `Flush()` per
+     event.
+  3. **Ad-hoc aggregations** (`/api/v1/knowledge/recent`,
+     `/api/v1/knowledge/content/{id}`, `/api/v1/activity/recent`,
+     `/api/v1/activity/session/{id}`, `/api/v1/learning/timeline`,
+     `/api/v1/learning/trend`) — return derived/aggregate shapes that don't
+     map cleanly to a schema type. If one of these stabilizes, promote it
+     to `openapi.yaml` with a proper schema and migrate the `serve*`
+     function to a strict handler.
+  The full list with reasons is in the "Non-OpenAPI routes" comment block
+  at the top of `NewHandler` in `server.go`.
 
 ## Testing philosophy
 

.agents/domains/knowledge/schema.md

@@ -1,48 +1,93 @@
 # Knowledge domain — schema
 
-The knowledge domain is the durable, authoritative current-state documentation of the homelab: one
-page per node and per cross-cutting system, synthesized from live state and evidence. It answers
-"what exists and how does it work right now."
+The knowledge domain is the durable, authoritative current-state documentation of the homelab:
+narrative for every node and cross-cutting system, synthesized from live state and evidence. It
+answers "what exists and how does it work right now."
 
 It follows the [LLM Wiki layer model](../../shared/llm-wiki.md) and the
 [writing-style](../../shared/writing-style.md) and [page-templates](../../shared/page-templates.md)
 rules.
 
-## The narrative / substrate split
+## Source of truth — the database
 
-The knowledge wiki is **narrative**. It sits alongside a **machine-readable substrate** that it
-describes but never contains. The split is load-bearing: several programs read the substrate at
-fixed paths, so the wiki reorganization never moves it.
+Per ADR 0003, the Postgres database is the single source of truth for all structured data **and**
+narrative knowledge. The narrative/substrate split of the Python era is gone: the DB holds both the
+structured graph (entities, relationships, status, metrics) and the narrative layer (documents,
+investigations, runbooks) in the `knowledge_entities` table.
 
-| Layer | Location | Consumed by |
-|-------|----------|-------------|
-| Substrate — source of truth | `inventory.yaml` (root) | MCP server, `homelab` CLI, `oikos/` scheduler/drift/relations/gen-topology |
-| Substrate — generated host records | `inventory.yaml` (root) | Go `internal/mcp/` server, `bin/homelab`; the single source of truth |
-| Substrate — kernel + context cards | `oikos/` (code, `oikos/cards/`, `oikos/state.json`) | MCP `explain`, scheduler |
-| Narrative — synthesized wiki | `archive/knowledge/{hosts,containers,vms,infrastructure}/` | humans, agents via MCP `get_page` / `search_docs` |
-| Evidence — immutable sources | `knowledge/sources/` (references + investigations) | synthesis into wiki pages |
+| Concern | Where it lives | How it gets there |
+|---------|----------------|-------------------|
+| Knowledge content — documents, investigations, runbooks | `knowledge_entities` table (rows linked to `entities` via `documents` / `about` edges) | Seeded from `seeds/knowledge.yaml` at deploy; mutated at runtime via the API |
+| Seed manifest (bootstrap + DR) | `seeds/knowledge.yaml` | Hand-edited or regenerated; ingested idempotently (content-hashed via `seed_versions`) |
+| Structured graph — hosts, services, entity types, relationships | `entities`, `relationships`, `entity_types` tables | Seeded from `seeds/{ontology,inventory}.yaml`; mutated via API/MCP |
+| Archived narrative wiki (read-only history) | `archive/knowledge/` | Frozen 2026-07-07 when the DB became source of truth |
 
-## Wiki pages
+### Seed ingest
 
-- **Node pages** (`archive/knowledge/containers/<id>-<name>.md`, `.../vms/<id>-<name>.md`,
-  `.../hosts/<name>.md`) follow the container/host template in
-  [page-templates.md](../../shared/page-templates.md): opening definition, `## At a glance`,
-  `## Role`, service/port map, storage, auto-deploy, `## Related`, `## Changelog`.
-- **Cross-cutting pages** (`archive/knowledge/infrastructure/<topic>.md`) follow the cross-cutting
-  template: `## Why`, `## Components`, `## How to apply`, `## Gotchas`, `## Related`, `## Changelog`.
-- Each `inventory.yaml` host entry carries a `doc_page:` field pointing at its narrative page.
-  Changing where a page lives means updating that field (read by `bin/homelab`).
+`seeds/knowledge.yaml` has three top-level lists — `documents`, `investigations`, `runbooks` — each
+entry carrying `slug`, `title`, `content` (markdown), and tags. `internal/knowledge/seed.go`
+ingests each entry by:
+
+1. `getOrCreateEntity` — ensures the slug exists in `entities` (type `document` / `investigation` /
+   `runbook`).
+2. `upsertKnowledgeEntity` — writes the markdown body into `knowledge_entities`, keyed by
+   `content_hash` so re-ingest is a no-op when nothing changed.
+3. `createEdge` — links the knowledge entity to its subject(s) via `documents` (for `document`) or
+   `about` (for `investigation`) edges. Runbooks bind to an `entity_type` via `applies_to_type`
+   rather than to a single entity.
+
+### Runtime mutation
+
+Agents register or update knowledge through the API, not by editing the seed:
+
+- `POST /api/v1/knowledge/{entity_slug}` — upsert a document/investigation on an entity
+  (`upsert_knowledge` MCP tool).
+- `update_entity_attributes` — merge a discovered fact (IP, version, port) into an entity.
+- `create_relationship` — record a discovered edge (`depends-on`, `hosts`, `routes-to`).
+
+> **Export gap.** `oikos export` regenerates `seeds/{ontology,inventory,policy}.yaml` from the DB
+> for version control, but **not** `seeds/knowledge.yaml`. Knowledge added via the API today lives
+> only in the DB until someone hand-edits the seed. Tracked as a follow-up.
+
+## Knowledge kinds
+
+- **Documents** (`document` entities, linked via `documents` edges) — node and cross-cutting
+  narrative pages. Carry `at_glance` (structured attributes) and a parsed `changelog`. Follow the
+  container / cross-cutting templates in [page-templates.md](../../shared/page-templates.md).
+- **Investigations** (`investigation` entities, linked via `about` edges) — incident evidence,
+  written once at incident time. Sections: `## Summary`, `## Timeline`, `## Root cause`,
+  `## Mitigations applied`, `## Open questions`.
+- **Runbooks** (`runbook` entities, bound by `applies_to_type`) — repeatable procedures. Carry
+  `risk_class` and a JSON-schema-validated `procedure`. **Runbooks also live as `SKILL.md` files
+  under `.agents/skills/<name>/`** — the DB row is the policy/lifecycle framing, the SKILL.md is
+  the executable procedure the agent loads. See
+  [the operations schema](../operations/schema.md).
 
 ## The two logs
 
-- The per-page **`## Changelog`** records infrastructure changes and is machine-parsed
-  (`get_changelog`, the Oikos ledger). Keep the `### YYYY-MM-DD — title` shape.
-- **`knowledge/log.md`** is append-only and records *documentation-maintenance* operations only
-  (restructures, source ingests, lint sweeps): `## [YYYY-MM-DD] <op> | <summary>`. It never
-  duplicates the Oikos change ledger (`oikos/ledger.py`).
+- The per-document **`## Changelog`** records infrastructure changes to that node. Keep the
+  `### YYYY-MM-DD — title` shape so the parsed `changelog` field stays structured.
+- **`archive/knowledge/log.md`** is the append-only record of *documentation-maintenance*
+  operations on the legacy wiki (restructures, source ingests, lint sweeps):
+  `## [YYYY-MM-DD] <op> | <summary>`. It is frozen with the rest of `archive/knowledge/`; new
+  doc-maintenance operations are recorded in the DB audit trail instead.
+
+## Querying knowledge
+
+Use MCP, not grep:
+
+- `search_knowledge(query)` — ILIKE search over documents, investigations, and runbooks in
+  `knowledge_entities`.
+- `get_entity_knowledge(entity_slug)` — every document, investigation, and runbook linked to one
+  entity, in one call.
+- `get_entity(slug)` / `get_relations(entity)` — the structured graph around an entity.
+
+Grep the clone only when MCP is unreachable, and prefer `archive/knowledge/` for historical
+narrative (it is not updated when the DB changes).
 
 ## Same-session update rule
 
-A change to a node updates every page that references it in the same session — the node page, the
-section `README.md` table, the root `README.md`, the Caddy/DNS/ingress pages, the host page, and
-`inventory.yaml`. See [page-templates.md](../../shared/page-templates.md#same-session-update-rule).
+A change to a node updates the DB in the same session — the entity's attributes, the relationships
+that reference it, and any document whose `at_glance` or changelog should reflect the new state. See
+[page-templates.md](../../shared/page-templates.md#same-session-update-rule) for the legacy wiki
+equivalent (now scoped to `archive/knowledge/` history).

.agents/domains/operations/schema.md

@@ -6,9 +6,10 @@ follows [writing-style](../../shared/writing-style.md); runbooks and plans use t
 exception.
 
 Where each kind lives: runbooks are skills under [`.agents/skills/`](../../skills/); operator
-reference (command cheatsheet, enrollment, Hermes agent) lives in
-[`.agents/operations/`](../../operations/); investigations are sources under
-`knowledge/sources/investigations/`; plans stay in the repo-root `plans/` folder (below).
+reference (command cheatsheet, enrollment, Nomos agent) lives in
+[`.agents/operations/`](../../operations/); investigations are `investigation` entities in the DB
+(historically `archive/knowledge/sources/investigations/`); plans stay in the repo-root `plans/`
+folder (below).
 
 ## Plans always live in `plans/`
 
@@ -21,7 +22,7 @@ message.** An agent drafting a plan:
 3. On completion, moves it to `plans/done/` and updates the index status.
 
 This is the single source for homelab design intent; keeping it in-repo means the plan is
-versioned, reviewable, and reachable by MCP `get_page`/`search_docs` like any other doc.
+versioned, reviewable, and reachable by MCP `search_knowledge` like any other doc.
 
 ## Runbooks
 
@@ -44,12 +45,14 @@ transition: "<from> -> <to>"   # only for lifecycle runbooks
 
 ## Investigations
 
-Incident records live in `knowledge/sources/investigations/YYYY-MM-DD-slug.md` and are **evidence sources** — written
-once at incident time, then linked from the changelogs of the nodes they implicate. Sections:
-`## Summary`, `## Timeline`, `## Root cause`, `## Mitigations applied`, `## Open questions`. Resolved
-incidents move to `knowledge/sources/investigations/archive/`.
+Incident records are `investigation` entities in the DB, linked to the entities they implicate via
+`about` edges. They are **evidence sources** — written once at incident time, then back-linked from
+the changelogs of the nodes they implicate. Sections: `## Summary`, `## Timeline`, `## Root cause`,
+`## Mitigations applied`, `## Open questions`. The legacy file-based investigations live at
+`archive/knowledge/sources/investigations/` (frozen 2026-07-07); new investigations go in the DB.
 
 ## The operations log
 
-`plans/log.md` and `knowledge/log.md` are append-only records of documentation operations on
-those areas (`## [YYYY-MM-DD] <op> | <summary>`), distinct from the Oikos change ledger.
+`plans/log.md` is the append-only record of documentation operations on plans
+(`## [YYYY-MM-DD] <op> | <summary>`), distinct from the DB audit trail. The legacy
+`archive/knowledge/log.md` is frozen with the rest of the archived wiki.

.agents/operations/commands.md

@@ -49,7 +49,7 @@ Run from the [hubris host](../../archive/knowledge/hosts/hubris.md) as root. Whe
 - `ras-mc-ctl --errors` — full event log
 - `cat /sys/devices/system/cpu/cpu0/cpufreq/energy_performance_preference` — should be `balance_power`
 - `cat /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor` — should be `powersave`
-- `ls /sys/fs/pstore/ /var/lib/systemd/pstore/` — panic traces from a previous crash (empty for pure hardware hangs — see [investigation](../../archive/knowledge/investigations/archive/2026-04-21-hubris-crash-loop.md))
+- `ls /sys/fs/pstore/ /var/lib/systemd/pstore/` — panic traces from a previous crash (empty for pure hardware hangs — see [investigation](../../archive/knowledge/investigations/2026-04-21-hubris-crash-loop.md))
 
 ## Fleet apt operations
 
@@ -67,7 +67,7 @@ the dpkg-interrupted recovery procedure specifically.
 
 See [OIKOS.md](../OIKOS.md) for the operating model. The `homelab` CLI this
 section used to document is retired; the actual current interface is the
-33 MCP tools cataloged in [AGENTS.md](../../AGENTS.md#3-the-mcp-server) plus
+MCP tool catalog in [AGENTS.md §3](../../AGENTS.md#3-the-mcp-server) plus
 the REST API. Closest current equivalents for what used to live here:
 
 | Old `homelab` command | Current equivalent |
@@ -82,7 +82,7 @@ the REST API. Closest current equivalents for what used to live here:
 
 There is no separately-deployed "Oikos Console" anymore — the control-room
 SPA (`web/`) is the operator dashboard, served standalone (see
-[plans/2026-07-12-wails-desktop-app.md](../../plans/2026-07-12-wails-desktop-app.md)).
+[plans/done/2026-07-12-wails-desktop-app.md](../../plans/done/2026-07-12-wails-desktop-app.md)).
 
 ## Related
 - [Hubris host](../../archive/knowledge/hosts/hubris.md)

.agents/shared/llm-wiki.md

@@ -1,40 +1,49 @@
 # LLM Wiki — the documentation contract
 
-How the narrative documentation in this repo is organized. The pattern is borrowed from the
-`sources / wiki / index / log` model: a durable synthesized layer (`archive/knowledge/`) built on top
-of immutable evidence (`knowledge/sources/`, incident records), with pure-listing indexes and an
-append-only operations log.
+How documentation in this repo is organized. The pattern is the `sources / wiki / index / log`
+model: a durable synthesized layer built on top of immutable evidence, with pure-listing indexes and
+an append-only operations log.
 
-This contract governs the **narrative layer only**. The machine-readable substrate — `inventory.yaml`,
-`secrets/`, `scripts/`, `bin/` — is not part of the wiki and never
-moves under it. See [the knowledge schema](../domains/knowledge/schema.md) for the split.
+This contract governs the **narrative layer only**. The machine-readable source of truth — the
+Postgres database, bootstrapped from `seeds/` — is not part of the wiki and never moves under it.
+See [the knowledge schema](../domains/knowledge/schema.md) for the split, and ADR 0003 for the
+DB-native model.
 
 ## Layers
 
-- **Sources** are immutable raw material: incident records (`knowledge/sources/investigations/`), external reference
-  docs (`knowledge/sources/references/`), and the live system itself (`pct config`, `docker inspect`).
-  Read them; do not rewrite them into other sources.
-- **Wiki** (`archive/knowledge/`) is the synthesized, authoritative current-state layer: one page per
-  node (`containers/`, `vms/`, host narratives) and per cross-cutting system (`infrastructure/`). A
-  reader understands the topic from the wiki page without reading the sources.
+- **Source of truth** is the Postgres database. Structured data (entities, relationships, status,
+  metrics) and narrative knowledge (documents, investigations, runbooks) both live there, in the
+  `entities` / `relationships` / `knowledge_entities` tables. It is bootstrapped at deploy time from
+  `seeds/{ontology,inventory,policy,knowledge}.yaml` (idempotent, content-hashed via
+  `seed_versions`) and mutated at runtime via the API/MCP. `oikos export` regenerates
+  `seeds/{ontology,inventory,policy}.yaml` for version control.
+- **Sources** are immutable raw material: incident records (now `investigation` entities in the DB,
+  historically `archive/knowledge/sources/investigations/`), external reference docs, and the live
+  system itself (`pct config`, `docker inspect`). Read them; do not rewrite them into other sources.
+- **Wiki** — the synthesized, authoritative current-state layer. Today this is the set of
+  `document` entities in the DB (one per node and per cross-cutting system), queried via MCP
+  `search_knowledge` / `get_entity_knowledge`. The legacy file-based wiki is frozen at
+  `archive/knowledge/{hosts,containers,vms,infrastructure}/` for historical reference only.
 - **Index** (`index.md` / folder `README.md`) is a pure listing — every page in scope with a
   one-line summary, and nothing else. Anything the section wants to say up front goes into a page
   the index lists, not into the index.
-- **Log** (`log.md`) is append-only, recording *doc-maintenance operations* (restructures, source
-  ingests, lint sweeps) in single-line format: `## [YYYY-MM-DD] <op> | <summary>`.
+- **Log** is append-only, recording *doc-maintenance operations* (restructures, source ingests,
+  lint sweeps) in single-line format: `## [YYYY-MM-DD] <op> | <summary>`. The active log is the DB
+  audit trail; `archive/knowledge/log.md` is the frozen legacy equivalent.
 
 ## Two logs, kept distinct
 
-- **`## Changelog`** on each node/topic page records *infrastructure* changes to that node. It is
-  machine-parsed (`get_changelog`, the Oikos ledger) — keep the `### YYYY-MM-DD — title` shape.
-- **`log.md`** per area records *documentation* operations only. It never duplicates the Oikos
-  change ledger (`oikos/ledger.py`), which stays authoritative for infra changes with
-  who/what/risk/approval/verification.
+- **`## Changelog`** on each node/topic document records *infrastructure* changes to that node. It
+  is stored as a structured field on the `document` entity — keep the `### YYYY-MM-DD — title`
+  shape so it parses cleanly.
+- **Doc-maintenance logs** record *documentation* operations only. They never duplicate the
+  infrastructure changelog, which stays authoritative for infra changes with
+  who/what/risk/approval/verification (now the DB audit trail, formerly `oikos/ledger.py`).
 
 ## Rules
 
 - Wiki pages stay short and focused. A page past ~300 lines splits.
-- Pages stay flat under `wiki/<section>/` until there are enough to warrant a sub-group.
+- Pages stay flat under their section until there are enough to warrant a sub-group.
 - Every page follows [writing-style.md](writing-style.md).
 - Plans and design docs always live in the repo `plans/` folder (`plans/YYYY-MM-DD-slug.md`),
   listed in `plans/index.md`, moved to `plans/done/` on completion — never a scratch path or a chat

.agents/shared/page-templates.md

@@ -9,12 +9,12 @@ in [writing-style.md](writing-style.md); the layer model (sources / wiki / index
 **Foundational / entry-point files:** ALL-CAPS
 
 - **Root level:** `AGENTS.md`, `README.md` — discovery paths for agents and humans.
-- **Agent instruction** (under `.agents/`): `OIKOS.md`, `HERMES.md` — foundational docs agents read before acting.
+- **Agent instruction** (under `.agents/`): `OIKOS.md`, `NOMOS.md` — foundational docs agents read before acting.
 - **Reference docs:** `GLOSSARY.md` — lookup reference (like classic repo conventions: LICENSE, CHANGELOG, GLOSSARY).
 
 **Content / narrative pages:** lowercase-with-dashes, date-prefixed as needed
 
-- **Container pages:** `<id>-<name>.md` (e.g. `101-jellyfin.md`, `132-rclone.md`). The `<id>` is the LXC/VM ordinal from `inventory.yaml`.
+- **Container pages:** `<id>-<name>.md` (e.g. `101-jellyfin.md`, `132-rclone.md`). The `<id>` is the LXC/VM ordinal from the entity's attributes in the DB (seeded via `seeds/inventory.yaml`).
 - **Infrastructure / cross-cutting pages:** `<topic>.md` (e.g. `dns.md`, `auto-deploy.md`, `mesh.md`). Describes a system, not a specific node.
 - **Plans / investigations:** `YYYY-MM-DD-<slug>.md` (e.g. `2026-07-05-oikos-prometheus-lxc.md`). Date-sorted; slug is lowercase.
 - **Section indices:** `README.md` (lowercase, conventional). Prefer in folders; `index.md` only if both intro prose and listing coexist.
@@ -118,7 +118,7 @@ What it looks like after.
 Changelog entries to write, index status to update.
 ```
 
-### Investigation (`knowledge/sources/investigations/YYYY-MM-DD-slug.md`)
+### Investigation (`investigation` entity in the DB; historically `archive/knowledge/sources/investigations/YYYY-MM-DD-slug.md`)
 
 ```markdown
 # YYYY-MM-DD — <title>
@@ -152,16 +152,18 @@ Changelog entries to write, index status to update.
 ## Same-session update rule
 
 When you make a change to a node — migrate an LXC, update an IP, change a
-mount, deploy a new service — **update every relevant doc page in the same
-session.** A change that touches a container page must also update:
+mount, deploy a new service — **update the DB and every relevant doc page in
+the same session.** A change that touches a container must also update:
 
-- The `containers/index.md` table (IPs, host, mounts, status)
+- The `entities` / `relationships` rows for the node (via the API/MCP) —
+  this is the source of truth
+- The `document` entity's `at_glance` and `## Changelog` for the container
+- The `containers/index.md` table in the archived wiki (IPs, host, mounts,
+  status) — historical reference, update for consistency where still consulted
 - The `README.md` table (if the change affects listed columns)
 - The Caddy page site list (if the change affects `*.hubris.network` routing)
 - The DNS / ingress infrastructure pages (if the change affects routing)
 - The `hosts/{hubris,strong}.md` host page (if container count changes)
-- The `inventory.yaml` host entry (single source of truth)
-- The `infrastructure/topology.md` (generated from inventory, but regen if needed)
 
 The pattern of updating only one page and leaving stale references on others
 is a bug. If you're doing a multi-step migration, document the intermediate

.agents/shared/writing-style.md

@@ -36,7 +36,7 @@ Every doc-level page follows the same shape so a reader scans it in one pass.
 1. **One H1 = the page title.** Node pages use `# <id> — \`<name>\``; topic pages use `# <Topic>`.
 2. **Opening definition.** First paragraph, 1–3 sentences, says what the thing is. No motivation, no marketing, no setup.
 3. **Body sections** in the natural order for the topic. Reuse the section templates in [page-templates.md](page-templates.md).
-4. **`## Changelog`** at the bottom of every node/topic page — reverse-chronological, append-only. This section is machine-parsed (Go MCP `get_changelog` in `internal/mcp/server.go`); keep the `### YYYY-MM-DD — title` shape.
+4. **`## Changelog`** at the bottom of every node/topic page — reverse-chronological, append-only. This section is stored as a structured field on the `document` entity in the DB; keep the `### YYYY-MM-DD — title` shape so it parses cleanly.
 5. **Related links** only at the bottom, only when a reference cannot be woven inline.
 
 ## Section indexes (folder READMEs)
@@ -53,12 +53,12 @@ duplicated prose, no narrative between the intro and the table.
 - Prefer **tables** for enumerable items with internal structure (service/port maps, field lists, status grids). Reserve bullets for short non-structured lists.
 - Use the **bold-leading-phrase pattern** for structured points: `**Read-only by construction.** The MCP server never mutates state.` — a bold noun phrase, a period, then the explanation.
 - When enumerating across services or nodes, give each its own `###` sub-section or a table row, not one run-on paragraph.
-- Use backticks for code, paths, hostnames, and file names (`inventory.yaml`, `192.168.8.77`, `pct config`); italics for first-mention terminology.
+- Use backticks for code, paths, hostnames, and file names (`seeds/inventory.yaml`, `192.168.8.77`, `pct config`); italics for first-mention terminology.
 - Use `>` blockquotes for caveats and gaps that interrupt the main flow: `> **Outstanding gap.** DNS-vs-inventory drift check not yet wired.` One thought per blockquote.
 
 ## Diagrams
 
-- Mermaid is the default for topology and flow diagrams. `infrastructure/topology.md` is generated by `oikos/gen-topology.py` — do not hand-edit it. (Go DB-native topology generation planned.)
+- Mermaid is the default for topology and flow diagrams. `infrastructure/topology.md` in the archived wiki was generated by the retired `oikos/gen-topology.py`; the DB-native equivalent is a future task — do not hand-edit the archived file expecting it to regenerate.
 - ASCII box diagrams are fine for small shape diagrams; keep them to one screen.
 
 ## Sourcing and cross-references

.agents/skills/knowledge-graph-audit/SKILL.md

@@ -0,0 +1,87 @@
+---
+name: knowledge-graph-audit
+risk_class: read_only
+inputs: []
+verification: "audit_knowledge_graph returns a report with summary.total_findings"
+docs_update_checklist: []
+---
+
+# Knowledge-graph audit
+
+Goal: validate that the knowledge graph (entities, relationships, checks) and
+the monitoring built on it reflect live reality — without mutating anything.
+Read-only. Run this before trusting health, blast-radius, or coverage answers,
+and whenever something feels off (a healthy host reports `down`, a retired
+service still alarms, the graph looks thin).
+
+## 1. Run the drift report
+
+Call MCP `audit_knowledge_graph` (or `GET /api/v1/audit/drift`). It returns a
+ranked list of findings, each with `{category, severity, count, entities,
+evidence, suggested_runbook}`, plus a `summary` with totals by category.
+
+The DB-side categories:
+
+- **orphan_checks** — check entities with truncated/random slugs left by the
+  old `shortSlug()` collision bug. Remediation: `scripts/cleanup-orphan-checks.sh`.
+- **dead_checks** — enabled `check_defs` whose target entity is `deprecated`/
+  `destroyed`. Remediation: `lifecycle-deprecate-node` / `lifecycle-destroy-node`
+  (the scheduler already skips these, but the rows should be retired).
+- **down_checks** — enabled probes reporting `down`. Remediation:
+  `service-health-check` (then check whether the failure is real or a
+  probe-config/routing problem — see step 3).
+- **unknown_checks** — probes that ran but reported `unknown` (usually a
+  misconfigured or not-yet-deployed probe script).
+- **unmonitored** — active entities whose type declares monitoring but have no
+  enabled `check_def`.
+- **dangling_edges** — live `hosts`/`provides`/`mounts` edges still pointing at
+  destroyed/deprecated targets. Remediation: `lifecycle-destroy-node`.
+
+## 2. Triage
+
+`severity: critical` (down_checks) first. For each finding, read `evidence` and
+open the entities with `get_entity` / `get_relations` to confirm the diagnosis
+before acting — the report is a pointer, not a verdict.
+
+## 3. Common probe-failure causes
+
+A `down_checks` finding that is NOT a real outage is usually one of:
+
+- **Guest reached wrong** — an LXC/VM check SSHed the guest directly instead of
+  routing through its Proxmox host. Confirm with `get_relations` that a `hosts`
+  edge exists and the guest has `pve_id`; checks route via `pct exec`/`qm guest
+  exec` automatically when both are present.
+- **Script not deployed** — the probe script is absent at `/opt/oikos/checks/`
+  inside the target. Remediation: redeploy via `tools/deploy-checks.sh`.
+- **macOS host** — a workstation check used the wrong SSH user or a Linux-only
+  script flag. The scheduler resolves `user: dtoro` from the entity attribute.
+
+## 4. What this audit does NOT cover (follow-ups)
+
+Live-infrastructure discovery has its own tool — run **`discover_infra_drift`**
+alongside this one. It compares running Proxmox guests (`pct`/`qm list` on every
+proxmox host) against the DB graph and returns:
+
+- **missing entities** — a guest running in Proxmox with no DB entity.
+- **ghost entities** — a DB lxc/vm whose `pve_id` is no longer live.
+
+Still manual until that machinery lands:
+
+- **Misplaced parent** — compare each guest's actual Proxmox host against its
+  `hosts` edge (migrations leave these stale).
+- **Undeployed scripts** — per-guest `/opt/oikos/checks/` presence.
+- **Unmodeled certs** — now modeled; verify with `audit_knowledge_graph` /
+  the cert-expiry checks.
+- **Seed drift** — run `oikos export` and `git diff seeds/` to find
+  runtime-created entities not in version control.
+
+## 5. Acting on findings
+
+This skill is read-only — make no changes here. Route each confirmed finding to
+its `suggested_runbook`, classify the action against `seeds/policy.yaml`, and
+proceed through the normal lifecycle/approval flow. Re-run the audit afterward
+to confirm the finding cleared.
+
+Docs-update checklist: none — the audit reads state; it changes nothing. If a
+finding reveals stale `risk_notes` or a wrong `doc_page`, fix `inventory.yaml`
+in that remediation session.

.claude/launch.json

@@ -5,7 +5,8 @@
       "name": "web",
       "runtimeExecutable": "sh",
       "runtimeArgs": ["-c", "export OIKOS_API_TOKEN=$(docker inspect -f '{{range .Config.Env}}{{println .}}{{end}}' oikos-api-1 | sed -n 's/^OIKOS_MCP_BEARER_TOKEN=//p'); exec npm --prefix web run dev"],
-      "port": 5173
+      "port": 5173,
+      "autoPort": true
     }
   ]
 }

.dockerignore

@@ -0,0 +1,12 @@
+# Every docker build in this repo previously sent the whole directory as
+# build context — including every OTHER git worktree under .claude/worktrees/
+# (each with its own web/node_modules, ~200-300MB apiece). That's what
+# starved the mac-mini's disk mid-build on 2026-07-27 (SHA 873b00a): the
+# context alone crossed 390MB of pure worktree cruft before the host ran out
+# of space. None of this ever belonged in an image.
+.claude/worktrees/
+.git/
+**/node_modules/
+**/dist/
+**/build/
+*.log

.gitea/workflows/ci.yml

@@ -70,3 +70,30 @@ jobs:
       - uses: actions/checkout@v4
       - name: docker build (verify image builds; no push)
         run: docker build -f compose/oikos/Dockerfile -t oikos:ci .
+
+  web:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: web
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
+        with:
+          node-version: '22'
+          cache: npm
+          cache-dependency-path: web/package-lock.json
+      - run: npm ci
+      - name: svelte-check (advisory — baseline not yet clean)
+        run: npm run check
+        continue-on-error: true
+      - name: eslint (advisory — baseline not yet clean)
+        run: npm run lint
+        continue-on-error: true
+      - name: prettier format check (advisory — baseline not yet clean)
+        run: npm run format:check
+        continue-on-error: true
+      - name: test
+        run: npm run test
+      - name: build
+        run: npm run build

.gitignore

@@ -24,3 +24,7 @@ cmd/desktop/build/
 cmd/desktop/Oikos
 desktop
 /eval
+
+# Local tooling artifacts (Playwright MCP session logs, stray screenshots)
+.playwright-mcp/
+config-screen.png

.golangci.yml

@@ -0,0 +1,41 @@
+# golangci-lint configuration for Oikos
+# Docs: https://golangci-lint.run/usage/configuration/
+run:
+  timeout: 5m
+  tests: true
+
+linters:
+  enable:
+    - govet        # go vet
+    - staticcheck  # advanced static analysis
+    - ineffassign  # detect ineffectual assignments
+    - unused       # find unused identifiers
+    - errcheck     # check for unchecked errors
+    - gosimple     # simplifications
+    - typecheck    # standard type checking
+    - misspell     # find commonly misspelled English words in comments
+    - revive       # fast, configurable linter (replaces golint)
+
+linters-settings:
+  errcheck:
+    # Allow unchecked errors on common Close/Flush patterns (deferred cleanup)
+    exclude-functions:
+      - (io.Closer).Close
+      - (*os.File).Close
+
+issues:
+  # Exclude generated code
+  exclude-rules:
+    - path: _test\.go
+      linters:
+        - errcheck
+    - path: internal/httpapi/gen/
+      linters:
+        - all
+    - path: internal/db/sqlcgen/
+      linters:
+        - all
+  # Don't auto-exclude common patterns
+  exclude-use-default: false
+  max-issues-per-linter: 0
+  max-same-issues: 0

AGENTS.md

@@ -1,7 +1,7 @@
 # AGENTS.md — orientation for any agent on a homelab client
 
 You are running on a machine that is part of the **hubris** homelab. The full
-context is in this checkout at `/opt/homelab-context/`. This file is the entry
+context is in this checkout at `/opt/homelab/`. This file is the entry
 point. Read it once at start, then keep working.
 
 - **New client?** Read [CLIENTS.md](CLIENTS.md) first.
@@ -30,7 +30,7 @@ is archived at `archive/knowledge/` for historical reference.
 
 Run `hostname` (Linux) or `scutil --get LocalHostName` (macOS), then read:
 
-    /opt/homelab-context/inventory.yaml
+    /opt/homelab/inventory.yaml
 
 That file tells you your role, your peers, what's mounted, and what services
 you host. If it does not exist, this client was not enrolled — stop and tell
@@ -39,12 +39,13 @@ the operator; see [CLIENTS.md](CLIENTS.md#enrollment) for the enrollment flow
 
 ## 2. The topology
 
-- `/opt/homelab-context/inventory.yaml` — every host, LXC, VM, and workstation
+- `/opt/homelab/inventory.yaml` — every host, LXC, VM, and workstation
   with their mesh addresses, roles, and service mappings. This is the seed file;
   at runtime the DB is authoritative (query via MCP `get_entity` or the REST API).
-- `/opt/homelab-context/seeds/knowledge.yaml` — full narrative knowledge: 36
-  documents, 6 investigations, 12 runbooks. Ingested into the DB on deploy.
-- `/opt/homelab-context/.agents/operations/commands.md` — the operator's cheatsheet
+- `/opt/homelab/seeds/knowledge.yaml` — full narrative knowledge
+  (documents, investigations, runbooks). Counts are not hardcoded here; count
+  them from the seed or query the DB. Ingested into the DB on deploy.
+- `/opt/homelab/.agents/operations/commands.md` — the operator's cheatsheet
   for pct, caddy, DNS, and the Oikos command surface.
 
 ## 3. The MCP server
@@ -55,7 +56,8 @@ Endpoint: `https://mcp.hubris.network/mcp`. Every call needs
 enrollment and `/healthz` (see "Authentication" below for where the token
 comes from).
 
-Available tools (33 total):
+Available tools (the authoritative list — count them below if a number is
+needed; do not hardcode the count elsewhere):
 
   Context — observe + orient:
     get_entity(slug), list_entities(type, limit, cursor),
@@ -111,10 +113,9 @@ Available tools (33 total):
       operator approval, and destructive patterns (rm -rf, dd, mkfs,
       pct/qm destroy, DROP TABLE, reboot, curl-pipe-to-shell, ...) always
       need approval regardless of what you declare. This is the ONLY
-      mutation tool — `request_execution` was retired 2026-07-14.
-    `run` — the general execution primitive. Run any shell
-      (restart, systemctl, pct_exec, apt_upgrade, pct_create). Still the
-      route for those specific actions; policy-gated the same way `run` is.
+      mutation tool — `request_execution` was retired 2026-07-14; the
+      former enum actions (restart, systemctl, pct_exec, apt_upgrade,
+      pct_create) are all expressed as `run(target, command)` now.
     get_execution_status(execution_id) — poll progress
 
 **When to prefer MCP over grepping the clone:** always for knowledge queries.
@@ -145,8 +146,8 @@ POST /api/v1/knowledge/{entity_slug}
 {"title": "...", "content": "...", "tags": ["..."]}
 ```
 
-The DB is the truth. The old wiki files are in `knowledge/wiki/` pending archive
-per the DB-as-source-of-truth plan.
+The DB is the truth. The old wiki files are archived at `archive/knowledge/`
+(historical reference only — use MCP `search_knowledge` for live queries).
 
 - **Runbook procedures** live as `runbook` entities in the DB and as SKILL.md
   files under `.agents/skills/<name>/`. They carry `risk_class`, `procedure`
@@ -162,8 +163,8 @@ per the DB-as-source-of-truth plan.
 ## 6. Acting on the homelab
 
 - **Read state**: use MCP tools. Nomos (the AI agent) is the primary
-  operator interface — it has 33 MCP tools for observe/orient/decide/act
-  (§3).
+  operator interface — it routes to the MCP tool list in §3 for
+  observe/orient/decide/act.
 - **Actions** (restart, logs, apt, pct exec, or anything else): Nomos calls
   `run` (the general execution primitive) via MCP. `reversible_low`/read-only actions execute
   immediately; `config_mutation` and `destructive` actions are queued for
@@ -178,7 +179,7 @@ per the DB-as-source-of-truth plan.
 
 ## 7. Communication mode
 
-Read and apply `/opt/homelab-context/.agents/shared/caveman.md` (if present). It defines the lab's
+Read and apply `/opt/homelab/.agents/shared/caveman.md` (if present). It defines the lab's
 terse-communication standard — drop filler, keep substance, use fragments.
 
 ## 8. Auto-setup mechanism
@@ -191,16 +192,15 @@ on every client after `git pull`. This is handled by `tools/post-pull.sh`
 Currently auto-setup:
 - **Host checks** (`tools/setup-checks.sh`): Deploys `checks/install.sh`'s
   health-check scripts to `/opt/oikos/checks` on each host. The scheduler's
-  `ssh-script` check kind depends on these actually being there — 20 are
-  live in the DB as of 2026-07-12.
+  `ssh-script` check kind depends on these actually being there (count is
+  whatever is currently seeded in the DB — do not hardcode it here).
 
 To add a new auto-setup, create `tools/setup-<name>.sh` in the repo,
 commit and push. All enrolled clients pick it up within 5 minutes.
 
 To trigger sync manually: run `/opt/homelab/tools/context-poller.sh`, or
-wait for the 5-min timer. (This mechanism — and the server-side
-`tools_changed` detection behind it — only correctly recognized
-`setup-*.sh` scripts as of 2026-07-12; before that it silently matched
+wait for the 5-min timer. (The server-side `tools_changed` detection only
+correctly recognizes `setup-*.sh` scripts — earlier it silently matched
 nothing, so nothing auto-ran on any client via this path.)
 
 ## 9. Versioning

CONTRIBUTING.md

@@ -51,7 +51,7 @@ The app stores credentials via `github.com/zalando/go-keyring` (service: `com.hu
 - Checks Gitea releases every 6 hours
 - System tray → **Check for Updates** triggers an immediate check
 - Download, extract, replace the app in `/Applications`, and relaunch
-- Versions are compared against the `version` const in `main.go`
+- Versions are compared against the `version` var in `main.go`, injected from the repo `VERSION` file at link time (`make desktop` passes `-ldflags "-X main.version=$(cat VERSION)"`)
 
 ## Project structure
 

Makefile

@@ -1,9 +1,10 @@
 .PHONY: build webhook test test-db lint generate generate-check dev migrate seed export clean tidy ui desktop desktop-package install
 
-BINARY := oikos
+BINARY := bin/oikos
 GO ?= go
 
 build:
+	mkdir -p bin
 	$(GO) build -o $(BINARY) -tags timetzdata ./cmd/oikos
 
 webhook:
@@ -19,9 +20,18 @@ test-db:
 	OIKOS_TEST_DATABASE_URL="postgres://oikos:$${OIKOS_DB_PASSWORD:-oikos_dev}@localhost:5432/oikos?sslmode=disable" \
 		$(GO) test -race -count=1 ./internal/db/ ./internal/httpapi/ ./internal/mcp/
 
-lint:
+lint: vet golangci govulncheck
+
+vet:
 	$(GO) vet ./...
-	@command -v golangci-lint >/dev/null 2>&1 && golangci-lint run || echo "golangci-lint not installed, skipping"
+
+golangci:
+	@command -v golangci-lint >/dev/null 2>&1 && golangci-lint run --config .golangci.yml || echo "golangci-lint not installed — see https://golangci-lint.run/usage/install/"
+
+govulncheck:
+	@command -v govulncheck >/dev/null 2>&1 && govulncheck ./... || echo "govulncheck not installed — run: go install golang.org/x/vuln/cmd/govulncheck@latest"
+
+.PHONY: lint vet golangci govulncheck
 
 generate:
 	$(GO) run github.com/oapi-codegen/oapi-codegen/v2/cmd/oapi-codegen@v2.4.1 \
@@ -56,7 +66,7 @@ desktop: ui   ## Build the Wails desktop app for the current platform
 	rm -rf cmd/desktop/frontend/dist
 	mkdir -p cmd/desktop/frontend/dist
 	cp -r web/dist/* cmd/desktop/frontend/dist/
-	cd cmd/desktop && CGO_ENABLED=1 go build -o build/bin/Oikos .
+	cd cmd/desktop && CGO_ENABLED=1 go build -ldflags "-X main.version=$$(cat ../VERSION)" -o build/bin/Oikos .
 
 desktop-package: desktop   ## Build + package the desktop app (zip on macOS, tar.gz on Linux)
 	@case $$(uname -s) in \
@@ -67,7 +77,7 @@ desktop-package: desktop   ## Build + package the desktop app (zip on macOS, tar
 			mkdir -p "$$APP/Contents/Resources"; \
 			cp cmd/desktop/build/bin/Oikos "$$APP/Contents/MacOS/Oikos"; \
 			cp cmd/desktop/icon.icns "$$APP/Contents/Resources/icon.icns"; \
-			sed 's/$$(VERSION)/0.1.0/' cmd/desktop/Info.plist.template > "$$APP/Contents/Info.plist"; \
+			sed "s/\$$(VERSION)/$$(cat VERSION)/" cmd/desktop/Info.plist.template > "$$APP/Contents/Info.plist"; \
 			cd cmd/desktop/build/bin && zip -r oikos-desktop-darwin-$$(uname -m).zip Oikos.app ;; \
 		Linux) \
 			cd cmd/desktop/build/bin && tar czf oikos-desktop-linux-$$(uname -m).tar.gz Oikos ;; \
@@ -81,6 +91,7 @@ install: desktop-package   ## Install to /Applications
 
 clean:
 	rm -f $(BINARY)
+	rm -rf bin
 	rm -rf cmd/desktop/build
 	rm -rf cmd/desktop/frontend/dist
 	$(GO) clean -testcache

README.md

@@ -49,7 +49,7 @@ cd web && OIKOS_API_TOKEN=dev-token npm run dev   # http://localhost:5173
 
 | Component | Port | Role |
 |-----------|------|------|
-| `oikos api` | 8090 | REST API + MCP server (15 tools) |
+| `oikos api` | 8090 | REST API + MCP server (tool list in [AGENTS.md §3](AGENTS.md#3-the-mcp-server)) |
 | `oikos scheduler` | — | Probe runner, signal lifecycle, metrics |
 | `oikos notifier` | — | Approval tokens, Matrix alerts |
 | `nomos serve` | 8092 | MCP client gateway, query routing |
@@ -112,8 +112,8 @@ oikos secret migrate  # SOPS → Infisical
 part of `docker-compose.yml`. It talks to `api`/`nomos` over HTTP with a
 bearer token entered on first launch (see `web/src/pages/Config.svelte`).
 Build with `make ui`, deploy with `make deploy-ui` (Caddy serves the static
-output). A native desktop wrapper is planned — see
-[plans/2026-07-12-wails-desktop-app.md](plans/2026-07-12-wails-desktop-app.md).
+output). A native desktop wrapper exists at `cmd/desktop/` — see
+[plans/done/2026-07-12-wails-desktop-app.md](plans/done/2026-07-12-wails-desktop-app.md).
 
 ## Repo layout
 
@@ -121,9 +121,10 @@ output). A native desktop wrapper is planned — see
 cmd/oikos/          Go entry point — single binary
 cmd/nomos/          Nomos MCP client gateway
 cmd/webhook/        Gitea deploy-webhook receiver (push-to-deploy on mac-mini)
-internal/           Go packages (httpapi, mcp, scheduler, actuator, learning,
-                    notifier, policy, secrets, db, config, ontology, domain,
-                    knowledge)
+cmd/desktop/        Wails desktop wrapper around the SPA
+internal/           Go packages (actuator, checkdefaults, config, db, domain,
+                    httpapi, knowledge, learning, mcp, notifier, observability,
+                    ontology, policy, safego, scheduler, secrets)
 web/                Control-room SPA (Svelte 5) — standalone, not embedded
 api/openapi.yaml    API contract (OpenAPI 3.1)
 migrations/         Forward-only SQL migrations (TimescaleDB)

VERSION

@@ -1 +1 @@
-0.7.6
+0.26.0

api/openapi.yaml

@@ -2284,6 +2284,23 @@ components:
           type: boolean
         version:
           type: integer
+        last_health:
+          type: string
+          description: >-
+            This check's own most recent verdict. An entity's health is the
+            worst of these across its enabled checks, so this is what explains
+            *why* an entity is degraded. Null until the check first runs.
+          nullable: true
+          enum:
+          - healthy
+          - degraded
+          - down
+          - unknown
+        last_run_at:
+          type: string
+          format: date-time
+          description: When this check last executed. Null = never run.
+          nullable: true
     CheckCreate:
       type: object
       required:

archive/knowledge/infrastructure/oikos-check-lifecycle.md

@@ -0,0 +1,104 @@
+# Oikos check lifecycle — how monitoring works
+
+This runbook covers how Oikos health checks are derived, created, and wired so
+an agent (Nomos) doesn't reverse-engineer source when asked to add monitoring to
+an entity — the problem that stranded session `23da10db` (2026-08-03).
+
+## Concepts
+
+- **`check_defs`** (scheduler config, table `check_defs`): the row the scheduler
+  reads to know *what* to probe and *when*. One per check instance.
+- **`check` entity** (type `check`, slug `check:<kind>:<target>:<n>`): the
+  knowledge-graph entity for that check. It carries attributes
+  (`check_type`, `target`, `port`, …) and `checks` edges to the probed target.
+- **`monitoring` spec** on an entity type (`entity_types.monitoring_spec`): the
+  default list of check kinds (e.g. `[http, process]` for `service`).
+  - Per-entity override: set `monitoring` in the entity's attributes —
+    `"none"` for zero checks, `["http"]` to replace the type defaults.
+- **`checkdefaults.Ensure`** (`internal/checkdefaults/defaults.go`): the
+  function that reads the monitoring spec, resolves host/port/URL from
+  attributes + relationships, and writes `check_defs` rows. Idempotent.
+
+## When checks are derived
+
+`checkdefaults.Ensure` runs in three situations (as of v0.17.1+):
+
+1. **Seed/deploy ingest** — `internal/db/seed.go:231`. Every entity gets its
+   default checks once on initial ingest.
+2. **HTTP `POST /api/v1/entities` (create)** — `ensureDefaultChecks` at
+   `internal/httpapi/impl.go:1012`. Creating an entity via the REST API derives
+   its checks in the same transaction.
+3. **HTTP `PATCH /api/v1/entities` (patch)** — `ensureDefaultChecks` at
+   `internal/httpapi/impl.go:1280`. Changing an entity's attributes (especially
+   `monitoring`) via the REST API regenerates its checks.
+4. **MCP `create_entity`** — SAME hook. Creating an entity via the MCP tool
+   derives checks. (Added 2026-08-03; previously MCP had no create.)
+5. **MCP `update_entity_attributes`** — SAME hook. Changing an entity's
+   `monitoring` attribute via MCP now regenerates checks. (Added 2026-08-03;
+   previously MCP updates silently skipped check derivation — the exact bug
+   that stranded the haos session.)
+
+## Check slug grammar
+
+```
+check:<kind>:<target-type>:<target-name>:<n>
+```
+
+Examples: `check:http:service:jellyfin:0`, `check:vm-status:vm:haos:0`,
+`check:cert-expiry:cert:house.hubris.network:0`.
+
+## Adding monitoring to an entity
+
+**If the entity already exists:**
+
+```
+update_entity_attributes(slug="service:haos", attributes={"monitoring":["http"]})
+```
+
+This regenerates checks via `checkdefaults.Ensure`. The result message tells you
+how many checks were derived and whether any kinds were skipped (and why).
+
+**If the entity does not exist yet (a new check, ingress, cert, etc.):**
+
+```
+create_entity(type="check", name="HAOS http check",
+  slug="check:http:service:haos:0",
+  attributes={"check_type":"http:service","target":"service:haos","port":"8123"})
+```
+
+This creates the entity AND derives its `check_defs`. Same for a new `ingress`
+(`type=ingress`, monitoring `[http]`) or `cert` (`type=cert`,
+monitoring `[cert-expiry]`).
+
+**To remove monitoring:** set `monitoring:["none"]` or transition the entity
+to a terminal lifecycle state (`set_entity_state` → `deprecated`/`destroyed`).
+
+## Caveats
+
+- **A service without a `url` attribute AND without a `probe_unit` gets no
+  process check** (the http check covers liveness; the process check would
+  be redundant without an opt-in `probe_unit`). The skip is logged.
+- **A service whose address comes from a `hosts` edge** may produce no checks on
+  initial create because the edge doesn't exist yet — the next inventory ingest
+  (or a later `update_entity_attributes` after the edge is created) fills it in.
+- **A `not found` error from `update_entity_attributes`** means the entity
+  doesn't exist — use `create_entity` instead.
+- **`check_defs` has target columns** (`target_id`, `target_type`). A check
+  entity needs a `checks` relationship (`create_relationship(source=check:…,
+  target=service:…, type="checks")`) so the scheduler can resolve what to
+  probe. `create_entity` derives the check_def; `create_relationship` links
+  the check entity to its target in the graph.
+
+## Related files
+
+- `internal/checkdefaults/defaults.go` — `Ensure`, `Target`, `LogResult`
+- `internal/httpapi/default_checks.go` — `ensureDefaultChecks` (HTTP hook)
+- `internal/db/checks.go` — `db.EnsureEntityChecks` (shared hook)
+- `internal/db/seed.go` — seed-time check derivation
+- `internal/mcp/tools.go` — `create_entity`, `update_entity_attributes`
+
+## Revision history
+
+- **2026-08-03:** Created after session `23da10db` stranded for lack of entity-
+  creation tool and unawareness of check-derivation triggers. Covers the MCP
+  create_entity + update_entity_attributes regen paths added same day.

checks/cpu_check.sh

@@ -2,12 +2,27 @@
 # cpu_check.sh — CPU usage % and thermal temperature.
 set -euo pipefail
 
-USAGE=$(top -bn1 2>/dev/null | awk '/^%Cpu/ {print 100 - $8}' || true)
-if [ -z "$USAGE" ]; then
-  CORES=$(nproc 2>/dev/null || sysctl -n hw.ncpu 2>/dev/null || echo 1)
-  USAGE=$(awk -v cores="$CORES" '{print ($1+$2+$3)*100/cores}' /proc/loadavg 2>/dev/null || echo "0")
+os=$(uname -s)
+
+if [ "$os" = "Darwin" ]; then
+  # `top -l 1 -n 0` prints "CPU usage: X% user, Y% sys, Z% idle".
+  # Usage is 100 minus the idle figure that precedes the literal `idle`.
+  USAGE=$(top -l 1 -n 0 -s 0 2>/dev/null | awk '
+    /^CPU usage/ {
+      for (i = 1; i <= NF; i++) {
+        if ($i == "idle") { gsub(/%/, "", $(i - 1)); printf "%.1f", 100 - $(i - 1) }
+      }
+    }' || true)
+else
+  USAGE=$(top -bn1 2>/dev/null | awk '/^%Cpu/ {print 100 - $8}' || true)
+  if [ -z "$USAGE" ]; then
+    CORES=$(nproc 2>/dev/null || sysctl -n hw.ncpu 2>/dev/null || echo 1)
+    USAGE=$(awk -v cores="$CORES" '{print ($1+$2+$3)*100/cores}' /proc/loadavg 2>/dev/null || echo "0")
+  fi
 fi
 
+[ -z "$USAGE" ] && USAGE=0
+
 TEMP=""
 if [ -f /sys/class/thermal/thermal_zone0/temp ]; then
   TEMP=$(awk '{printf "%.1f", $1/1000}' /sys/class/thermal/thermal_zone0/temp 2>/dev/null || true)

checks/disk_usage_check.sh

@@ -2,18 +2,34 @@
 # disk_usage_check.sh — disk usage and inode usage per mountpoint.
 set -euo pipefail
 
-MOUNTS=$(df -k 2>/dev/null | awk 'NR>1 && $1 ~ /^\// && $NF !~ /^\/(snap|dev|proc|sys|run|private)/ {print $NF}' || true)
+# `timeout` caps each df so a single hung/stale mountpoint (a stale NFS
+# export, a wedged ZFS pool) can't stall the whole check — that hung the
+# scheduler's 30s budget on hubris. Available on Linux (coreutils); absent on
+# Darwin, whose local mounts don't hang, so it degrades to an empty prefix.
+TO=""
+if command -v timeout >/dev/null 2>&1; then TO="timeout 8"; fi
+
+# Build the mount list WITHOUT statting anything: reading /proc/mounts never
+# blocks the way `df` does on a stuck filesystem, so the enumeration itself
+# can't hang. Fall back to `df` on hosts without /proc/mounts (macOS).
+if [ -r /proc/mounts ]; then
+  MOUNTS=$(awk '$1 ~ /^\// && $2 !~ /^\/(snap|dev|proc|sys|run|private)/ {print $2}' /proc/mounts || true)
+else
+  MOUNTS=$($TO df -k 2>/dev/null | awk 'NR>1 && $1 ~ /^\// && $NF !~ /^\/(snap|dev|proc|sys|run|private)/ {print $NF}' || true)
+fi
 FIRST=1
 
 echo -n '{"health":"healthy","metrics":{'
 for m in $MOUNTS; do
-  LINE=$(df -k "$m" 2>/dev/null | awk 'NR==2 {print $3, $4, $5, $7}' | tr -d '%' || true)
+  # Each df is bounded: a stuck mount times out and is skipped (LINE empty)
+  # rather than hanging the probe.
+  LINE=$($TO df -k "$m" 2>/dev/null | awk 'NR==2 {print $3, $4, $5, $7}' | tr -d '%' || true)
   if [ -z "$LINE" ]; then continue; fi
   USED=$(echo "$LINE" | awk '{print $1}')
   FREE=$(echo "$LINE" | awk '{print $2}')
   PCT=$(echo "$LINE" | awk '{print $3}')
 
-  INODE_LINE=$(df -i "$m" 2>/dev/null | awk 'NR==2 {print $5}' | tr -d '%' || echo "0")
+  INODE_LINE=$($TO df -i "$m" 2>/dev/null | awk 'NR==2 {print $5}' | tr -d '%' || echo "0")
   INODE_PCT=$(echo "${INODE_LINE:-0}" | sed 's/-/0/')
 
   KEY=$(echo "$m" | sed 's|/|_|g' | sed 's|^_||')

checks/process_check.sh

@@ -1,5 +1,17 @@
 #!/usr/bin/env bash
-# process_check.sh — systemd service liveness.
+# process_check.sh — service liveness.
+#
+# A service entity's name is a logical label, rarely the literal systemd unit
+# or container name. matrix = matrix-synapse.service + element-web/mautrix-*
+# containers; authentik = authentik-server/-worker containers. So checking
+# `systemctl is-active matrix` reports "inactive" for a healthy service.
+#
+# Resolution order, any hit = healthy:
+#   1. exact systemd unit  `systemctl is-active <name>`
+#   2. a systemd unit with the name as prefix  `<name>*.service`
+#   3. a running docker container whose name contains <name>
+# An explicit probe target overrides the label — see checkdefaults, which
+# passes a `probe_unit`/`container`/`systemd_unit` attribute as $1 when set.
 set -euo pipefail
 
 SERVICE="${1:-}"
@@ -8,15 +20,31 @@ if [ -z "$SERVICE" ]; then
   exit 0
 fi
 
-if ! command -v systemctl >/dev/null 2>&1; then
-  echo '{"health":"unknown","signalKind":"process-check","evidence":"systemctl not found"}'
-  exit 0
+ok() { echo "{\"health\":\"healthy\"}"; exit 0; }
+
+# 1. exact systemd unit
+if command -v systemctl >/dev/null 2>&1; then
+  STATE=$(systemctl is-active "$SERVICE" 2>/dev/null | head -1 || true)
+  [ "$STATE" = "active" ] && ok
+
+	# 2. prefix match: matrix -> matrix-synapse.service, house -> house.service, etc.
+	# --no-legend strips the header/footer so grep can see the unit rows; the
+	# pattern is a systemd unit glob.
+	if systemctl list-units --type=service --state=active --no-legend "$SERVICE*.service" 2>/dev/null \
+       | grep -q '\.service'; then
+    ok
+  fi
 fi
 
-STATE=$(systemctl is-active "$SERVICE" 2>/dev/null || echo "unknown")
-
-if [ "$STATE" = "active" ]; then
-  echo "{\"health\":\"healthy\"}"
-else
-  echo "{\"health\":\"degraded\",\"signalKind\":\"$SERVICE\",\"evidence\":\"$SERVICE is $STATE\"}"
+# 3. a running docker container whose name contains the label.
+if command -v docker >/dev/null 2>&1; then
+  if docker ps --filter "status=running" --filter "name=$SERVICE" --format '{{.Names}}' 2>/dev/null \
+       | grep -q .; then
+    ok
+  fi
 fi
+
+STATE=${STATE:-inactive}
+STATE=${STATE//\"/}
+SAFE_SERVICE=${SERVICE//\"/}
+echo "{\"health\":\"degraded\",\"signalKind\":\"process\",\"evidence\":\"$SAFE_SERVICE is $STATE (no active unit/container matched)\"}"

cmd/desktop/main.go

@@ -36,13 +36,17 @@ var iconPNG []byte
 const (
 	keyringService   = "com.hubris.oikos-desktop"
 	keyringUser      = "oikos"
-	version          = "0.1.0"
 	updateURL        = "https://git.hubris.network/api/v1/repos/dtoro/oikos/releases"
 	pollInterval     = 30 * time.Second
 	updateInterval   = 6 * time.Hour
 	oidcCallbackPort = 18901
 )
 
+// version is injected at link time via -ldflags "-X main.version=$(cat VERSION)"
+// (Makefile desktop target). The default keeps a non-empty fallback for
+// `go build ./cmd/desktop` without ldflags.
+var version = "0.1.0-dev"
+
 type OikosConfig struct {
 	ApiUrl    string `json:"apiUrl"`
 	Token     string `json:"token,omitempty"`

cmd/nomos/agent.go

@@ -57,6 +57,13 @@ type agent struct {
 	apiBase    string // oikos HTTP API base, derived from NOMOS_MCP_URL, for chat-assent approvals
 	apiToken   string // OIKOS_MCP_BEARER_TOKEN — api's combinedAuth requires it (no dev-open bypass)
 	httpClient *http.Client
+	// gate serializes turns per session (at most one in-flight turn per
+	// sessionID). See turngate.go and plan 2026-08-03 F1.
+	gate *turnGate
+	// queue holds operator messages that arrived while a turn was already
+	// running; they are auto-run when the gate frees (plan 2026-08-03 F2).
+	// See messagequeue.go.
+	queue *messageQueue
 }
 
 func newAgent(ctx context.Context, clients *mcpClientPool, st *store, agentSlug string) (*agent, error) {
@@ -117,6 +124,8 @@ func newAgent(ctx context.Context, clients *mcpClientPool, st *store, agentSlug
 		apiBase:    apiBase,
 		apiToken:   os.Getenv("OIKOS_MCP_BEARER_TOKEN"),
 		httpClient: &http.Client{Timeout: 15 * time.Second},
+		gate:       newTurnGate(),
+		queue:      newMessageQueue(),
 	}, nil
 }
 
@@ -168,10 +177,15 @@ type toolDef struct {
 }
 
 type agentEvent struct {
-	Type       string `json:"type"`
-	Data       any    `json:"data,omitempty"`
-	SessionID  string `json:"session_id,omitempty"`
-	Iteration  int    `json:"iteration,omitempty"`
+	Type      string `json:"type"`
+	Data      any    `json:"data,omitempty"`
+	SessionID string `json:"session_id,omitempty"`
+	Iteration int    `json:"iteration,omitempty"`
+	// IsThinking marks text/text_delta events that carry the model's internal
+	// reasoning (text produced before tool calls in the same iteration), as
+	// distinct from the final response text. The frontend renders these as
+	// collapsible thinking blocks separated from the response.
+	IsThinking bool `json:"is_thinking,omitempty"`
 }
 
 func (a *agent) chat(ctx context.Context, sessionID, message string, emit func(agentEvent)) {
@@ -349,6 +363,15 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 		messages = append(messages, openai.SystemMessage(systemInject))
 	}
 
+	// Retry cap (P0.1 from plans/2026-07-18-session-review-three-sessions.md):
+	// track failing `run` calls within this turn so an identical command that
+	// keeps failing is refused after maxRunRetries attempts. Without this,
+	// session 1e9c7691 retried the same `chown` ~20 times, each retry piling
+	// up a zombie process on the target (knfsd was holding a kernel lock).
+	// The tracker is per-turn — a fresh turn after the operator responds can
+	// retry once more, so this doesn't permanently block recovery.
+	retries := newRunRetryTracker()
+
 	for i := 0; i < maxIterations; i++ {
 		params := openai.ChatCompletionNewParams{
 			Model:    openai.ChatModel(a.model),
@@ -359,7 +382,12 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 		var msg openai.ChatCompletionMessage
 		var acc openai.ChatCompletionAccumulator
 
-		for attempt := 0; attempt <= maxLLMRetries; attempt++ {
+		// Capture token usage from this LLM response for activity logging.
+	// Previously always NULL — every agent_activity row had no token
+	// count. Now each tool call in this iteration gets the same total.
+	totalTokens := 0
+
+	for attempt := 0; attempt <= maxLLMRetries; attempt++ {
 			acc = openai.ChatCompletionAccumulator{}
 			stream := a.provider.Chat.Completions.NewStreaming(ctx, params, a.reqOpts...)
 			for stream.Next() {
@@ -391,14 +419,19 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			msg = acc.Choices[0].Message
 			finishReason := acc.Choices[0].FinishReason
 
+			// Capture token usage from this iteration.
+			if acc.Usage.TotalTokens > 0 {
+				totalTokens = int(acc.Usage.TotalTokens)
+			}
+
 			if len(msg.ToolCalls) == 0 {
 				if isRefusalOrEmpty(msg.Content) {
-					if attempt < maxLLMRetries {
-						slog.Warn("nomos: empty or refusal response, retrying",
-							"session", sessionID, "iter", i+1, "attempt", attempt+1,
-							"content_len", len(msg.Content), "finish_reason", finishReason)
-						continue
-					}
+				if attempt < maxLLMRetries {
+					slog.Warn("nomos: empty or refusal response, retrying",
+						"session", sessionID, "iter", i+1, "attempt", attempt+1,
+						"content_len", len(msg.Content), "finish_reason", finishReason)
+					continue
+				}
 					// B.4: surface the real error context (finish_reason +
 					// refusal text) instead of a generic "empty response" —
 					// the operator can tell "content_filter — rephrase" from
@@ -447,7 +480,7 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 		// led to each step. Emitting it lets the persist layer accumulate
 		// per-iteration reasoning into the row's text field.
 		if strings.TrimSpace(msg.Content) != "" {
-			emit(agentEvent{Type: "text", Data: msg.Content, SessionID: sessionID})
+			emit(agentEvent{Type: "text", Data: msg.Content, SessionID: sessionID, IsThinking: true})
 		}
 
 		slog.Info("nomos: tool calls", "count", len(msg.ToolCalls), "iter", i+1, "correlation", correlationID)
@@ -467,6 +500,33 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 				sawCompleteTask = true
 			}
 
+			// Retry cap: if this `run` call has already failed
+			// maxRunRetries times this turn with the same (target,
+			// command), refuse to dispatch it again. Return a synthetic
+			// tool result directing the agent to investigate *why* the
+			// command hangs instead of retrying. See retrycap.go and
+			// plans/2026-07-18-session-review-three-sessions.md P0.1.
+			if tc.Function.Name == "run" {
+				t, _ := args["target"].(string)
+				c, _ := args["command"].(string)
+				key := runFailureKey(t, c)
+				if n := retries.failures(key); n >= maxRunRetries {
+					directive := runRetryDirective(t, c, n)
+					slog.Warn("nomos: run retry cap hit — refusing dispatch",
+						"target", t, "failures", n, "session", sessionID)
+					a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args,
+						tc.Function.Arguments, directive, 0, false, correlationID, totalTokens)
+					emit(agentEvent{
+						Type:      "tool_result",
+						Data:      map[string]any{"name": tc.Function.Name, "result": directive, "id": tc.ID, "retry_capped": true},
+						SessionID: sessionID,
+						Iteration: i + 1,
+					})
+					messages = append(messages, openai.ToolMessage(directive, tc.ID))
+					continue
+				}
+			}
+
 			emit(agentEvent{
 				Type:      "tool_use",
 				Data:      map[string]any{"name": tc.Function.Name, "args": args, "id": tc.ID},
@@ -506,7 +566,23 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			inputStr := string(inputJSON)
 
 			if callErr != nil {
-				a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, callErr.Error(), elapsed, false, correlationID)
+				a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, callErr.Error(), elapsed, false, correlationID, totalTokens)
+
+				// Retry cap: dispatch errors (e.g. MCP client timeout)
+				// count toward the cap too. A command that keeps timing
+				// out at the gateway is exactly the pattern we want to
+				// break — see session 1e9c7691's 20+ identical
+				// `chown` timeouts.
+				if tc.Function.Name == "run" {
+					t, _ := args["target"].(string)
+					c, _ := args["command"].(string)
+					key := runFailureKey(t, c)
+					n := retries.recordFailure(key)
+					if n >= maxRunRetries {
+						slog.Warn("nomos: run failure cap reached — next identical call will be refused",
+							"target", t, "failures", n, "session", sessionID)
+					}
+				}
 
 				emit(agentEvent{
 					Type:      "tool_result",
@@ -520,7 +596,7 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			}
 
 			resultJSON, _ := json.Marshal(result)
-			a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, string(resultJSON), elapsed, true, correlationID)
+			a.store.logActivity(ctx, a.agentID, sessionID, tc.Function.Name, args, inputStr, string(resultJSON), elapsed, true, correlationID, totalTokens)
 
 			// Link any execution this tool queued/started back to this
 			// session, so the auto-continuation worker can feed its result
@@ -551,6 +627,25 @@ func (a *agent) chatWith(ctx context.Context, sessionID, message, systemInject s
 			messages = append(messages, openai.ToolMessage(string(resultJSON), tc.ID))
 			slog.Info("nomos: tool success", "tool", tc.Function.Name, "ms", elapsed)
 
+			// Retry cap: record failures of `run` calls so the cap above
+			// can refuse a repeated identical failure. A "failure" here
+			// means the dispatch errored OR the MCP result text matches
+			// the "run on <target>: ERROR …" signature — both indicate
+			// the command actually ran and failed, not just that it
+			// queued for approval (pending approvals are not failures).
+			// Pass the RAW result text (not JSON-encoded) so the helper's
+			// HasPrefix check sees "run on …" not "\"run on …\"".
+			if isRunFailure(tc.Function.Name, runResultText(result), callErr) {
+				t, _ := args["target"].(string)
+				c, _ := args["command"].(string)
+				key := runFailureKey(t, c)
+				n := retries.recordFailure(key)
+				if n >= maxRunRetries {
+					slog.Warn("nomos: run failure cap reached — next identical call will be refused",
+						"target", t, "failures", n, "session", sessionID)
+				}
+			}
+
 			// ask_operator pauses the task: the agent has posed a decision only
 			// the operator can make. End the turn here so it doesn't barrel past
 			// its own question — the answer (panel or chat reply) resumes it.

cmd/nomos/continue.go

@@ -76,16 +76,20 @@ func (a *agent) processIdleSweep(ctx context.Context) {
 		s := s
 		if s.CompletionNudges == 0 {
 			safego.Go("nomos:idle-nudge:"+s.ID, func() {
-				if err := a.store.bumpCompletionNudge(ctx, s.ID); err != nil {
-					slog.Error("nomos: idle nudge bump failed", "session", s.ID, "error", err)
-					return
+				note := fmt.Sprintf("[System: this task ('%s') has been idle for %s with no complete_task call. "+
+					"If the goal is done (or can't be completed), call complete_task now with the outcome and a "+
+					"one-line summary. If you're still genuinely working through the plan, ignore this and continue.]",
+					s.Goal, idleTaskThreshold)
+				note = a.store.enrichResumeNote(ctx, s.ID, note)
+				// P1: only count the nudge if it actually delivered. resumeSession
+				// skips (returns false) when a turn is already active; bumping the
+				// counter anyway would make the next sweep auto-close a merely-busy
+				// session as "unanswered."
+				if a.resumeSession(ctx, s.ID, note) {
+					if err := a.store.bumpCompletionNudge(ctx, s.ID); err != nil {
+						slog.Error("nomos: idle nudge bump failed", "session", s.ID, "error", err)
+					}
 				}
-			note := fmt.Sprintf("[System: this task ('%s') has been idle for %s with no complete_task call. "+
-				"If the goal is done (or can't be completed), call complete_task now with the outcome and a "+
-				"one-line summary. If you're still genuinely working through the plan, ignore this and continue.]",
-				s.Goal, idleTaskThreshold)
-			note = a.store.enrichResumeNote(ctx, s.ID, note)
-			a.resumeSession(ctx, s.ID, note)
 			})
 			continue
 		}
@@ -163,7 +167,9 @@ func (a *agent) processContinuations(ctx context.Context) {
 				continue
 			}
 		}
-		a.store.markContinued(ctx, p.ExecID) // stamp first: a failure here must not cause a re-continue loop
+		// markContinued now happens inside continueSession, AFTER resumeSession
+		// actually runs (P0). Pre-marking here consumed the item even when
+		// resumeSession skipped on a busy session, losing the result.
 		safego.Go("nomos:continue-session:"+p.SessionID, func() { a.continueSession(ctx, p) })
 	}
 }
@@ -179,7 +185,18 @@ func (a *agent) processContinuations(ctx context.Context) {
 // something new to poll for.
 func (a *agent) continueSession(ctx context.Context, p pendingContinuation) {
 	slog.Info("nomos: auto-continuing session", "session", p.SessionID, "execution", p.ExecID, "status", p.Status)
-	a.resumeSession(ctx, p.SessionID, buildContinuationNote(p))
+	// P0 (plans/2026-08-03-nomos-chat-changes-review.md): mark the execution
+	// continued ONLY after the turn actually ran. resumeSession skips (returns
+	// false) when another turn is already active for this session; marking
+	// before that — as the old code did — consumed the item (continued_at set,
+	// never re-queued by pendingContinuations) and silently lost the result.
+	// On a skip, leave it pending so the next worker tick retries once the
+	// active turn frees the permit.
+	if !a.resumeSession(ctx, p.SessionID, buildContinuationNote(p)) {
+		slog.Info("nomos: continuation deferred — a turn is active; will retry next tick", "session", p.SessionID, "execution", p.ExecID)
+		return
+	}
+	a.store.markContinued(ctx, p.ExecID)
 }
 
 // resumeSession re-invokes the agent for a session with a system-injected note —
@@ -187,7 +204,32 @@ func (a *agent) continueSession(ctx context.Context, p pendingContinuation) {
 // (handleAnswerQuestion) — persisting progress LIVE (a placeholder row updated
 // in place as each tool call lands) so the frontend poller sees each step,
 // instead of total silence until the whole resume concludes.
-func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
+//
+// F1 (plan 2026-08-03): this is the single entry point for EVERY background
+// turn — the continuation worker, idle sweep, answer-question, /resume, and the
+// empty-message reconnect all funnel through here. It acquires the session's
+// turn permit non-blocking and SKIPS if a turn is already running. A duplicate
+// resume while a turn (live or background) is active is exactly the
+// interleaving that corrupted the activity panel and made tasks feel stuck.
+//
+// Returns whether the turn actually ran. Callers that mutate state before
+// resuming (the continuation worker's markContinued, the idle sweep's nudge
+// bump) MUST gate that mutation on a true return — otherwise a busy-skip leaves
+// the state changed but the work undone (lost continuation / false auto-close).
+// See plans/2026-08-03-nomos-chat-changes-review.md P0/P1.
+func (a *agent) resumeSession(ctx context.Context, sessionID, note string) bool {
+	if !a.gate.acquire(sessionID, 0) {
+		slog.Info("nomos: turn already active, skipping background resume", "session", sessionID)
+		return false
+	}
+	// Release the gate, then drain any operator message that was queued while
+	// this background turn ran (plan 2026-08-03 F2). Queued messages are run as
+	// real user turns server-side; resumeSession itself never enqueues.
+	defer func() {
+		a.gate.release(sessionID)
+		safego.Go("nomos:drain:"+sessionID, func() { a.drainQueued(context.Background(), sessionID) })
+	}()
+
 	placeholder, _ := json.Marshal(map[string]any{
 		"role": "assistant",
 		"text": "",
@@ -200,6 +242,7 @@ func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
 
 	var toolCalls []map[string]any
 	var finalText, errText string
+	var finalThinking string
 
 	persist := func() {
 		if msgID == uuid.Nil {
@@ -212,6 +255,7 @@ func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
 		body, _ := json.Marshal(map[string]any{
 			"role":       "assistant",
 			"text":       text,
+			"thinking":   finalThinking,
 			"tool_calls": toolCalls,
 			"auto":       true, // marks this as an autonomous continuation, not an operator turn
 		})
@@ -242,15 +286,19 @@ func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
 		if attempt > 0 {
 			select {
 			case <-cctx.Done():
-				return
+				return true // a turn ran on an earlier attempt; consume, don't re-loop
 			case <-time.After(time.Duration(2<<attempt) * time.Second): // 4s, 8s
 			}
 		}
 		toolCalls, finalText, errText = nil, "", ""
+		finalThinking = ""
 		// P3: accumulate per-iteration reasoning instead of overwriting
 		// (same fix as main.go's chat handler). Without this, a resumed
 		// turn's intermediate thinking is lost on reload.
+		// (same fix as main.go's chat handler). Without this, a resumed
+		// turn's intermediate thinking is lost on reload.
 		var textParts []string
+		var thinkingParts []string
 		emit := func(ev agentEvent) {
 			if ev.Type == "tool_use" || ev.Type == "tool_result" {
 				if m, ok := ev.Data.(map[string]any); ok {
@@ -277,8 +325,13 @@ func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
 			}
 			if ev.Type == "text" {
 				if t, ok := ev.Data.(string); ok && t != "" {
-					textParts = append(textParts, t)
-					finalText = strings.Join(textParts, "\n\n")
+					if ev.IsThinking {
+						thinkingParts = append(thinkingParts, t)
+						finalThinking = strings.Join(thinkingParts, "\n\n")
+					} else {
+						textParts = append(textParts, t)
+						finalText = strings.Join(textParts, "\n\n")
+					}
 					persist()
 				}
 			}
@@ -314,9 +367,10 @@ func (a *agent) resumeSession(ctx context.Context, sessionID, note string) {
 			// No placeholder was inserted (rare), save directly.
 			a.store.saveMessage(context.Background(), sessionID, "assistant", body)
 		}
-		return // do not call persist() again — already persisted above
+		return true // do not call persist() again — already persisted above
 	}
 	persist() // final state — same row, updated one last time with the concluding text
+	return true
 }
 
 // buildContinuationNote frames the finished execution for the model: what

cmd/nomos/continue_test.go

@@ -1,6 +1,11 @@
 package main
 
-import "testing"
+import (
+	"context"
+	"testing"
+
+	"github.com/google/uuid"
+)
 
 func TestExtractExecutionIDs(t *testing.T) {
 	// Real tool-result phrasings that should yield an execution id.
@@ -37,3 +42,37 @@ func TestExtractExecutionIDs(t *testing.T) {
 		t.Errorf("expected de-dup to 1 id, got %v", ids)
 	}
 }
+
+// TestResumeSession_SkipsWhenBusy guards the P0 fix
+// (plans/2026-08-03-nomos-chat-changes-review.md): resumeSession must skip —
+// return false, body never executed — when a turn is already active for the
+// session. continueSession relies on this so it only marks a continuation
+// "continued" after a turn really ran (otherwise the result is lost: marked
+// continued, never re-queued by pendingContinuations).
+//
+// A minimal agent with only a gate is enough: if the body ever ran, chatWith
+// would dereference the nil provider and panic. Returning false cleanly proves
+// the body was skipped.
+func TestResumeSession_SkipsWhenBusy(t *testing.T) {
+	a := &agent{gate: newTurnGate()}
+	if !a.gate.acquire("sess", 0) {
+		t.Fatal("precondition: initial acquire should succeed on a free session")
+	}
+	ran := a.resumeSession(context.Background(), "sess", "note")
+	if ran {
+		t.Fatal("resumeSession must return false (skip) while a turn is active for the session")
+	}
+}
+
+// TestContinueSession_DefersWhenBusy guards the other half of P0: when the
+// session is busy, continueSession defers (leaves the execution pending for the
+// next worker tick) instead of running or marking it. It must return cleanly
+// without reaching resumeSession's body (nil provider → panic) or markContinued.
+func TestContinueSession_DefersWhenBusy(t *testing.T) {
+	a := &agent{gate: newTurnGate()}
+	if !a.gate.acquire("sess", 0) {
+		t.Fatal("precondition: initial acquire should succeed on a free session")
+	}
+	p := pendingContinuation{ExecID: uuid.New(), SessionID: "sess", Status: "completed"}
+	a.continueSession(context.Background(), p) // must not panic; must not run/mark
+}

cmd/nomos/eval/main.go

@@ -319,8 +319,10 @@ func fetchTranscript(ctx context.Context, gateway, sid string) (transcript, sess
 	}
 	// Fetch the plan (steps with generation numbers) for the
 	// plan_generations assertion. A 404 or empty response is fine — a
-	// pure-DB Q&A with no propose_plan has no plan.
-	if planResp, perr := http.Get(gateway + "/sessions/" + sid + "/plan"); perr == nil {
+	// pure-DB Q&A with no propose_plan has no plan. ?all=true returns every
+	// generation so the assertion can count them (the default view returns
+	// only the current generation).
+	if planResp, perr := http.Get(gateway + "/sessions/" + sid + "/plan?all=true"); perr == nil {
 		if planResp.StatusCode == 200 {
 			pb, _ := io.ReadAll(planResp.Body)
 			_ = json.Unmarshal(pb, &t) // fills t.PlanSteps via "steps" field

cmd/nomos/main.go

@@ -11,6 +11,7 @@ import (
 	"net/http"
 	"os"
 	"os/signal"
+	"strconv"
 	"strings"
 	"sync"
 	"syscall"
@@ -18,6 +19,7 @@ import (
 
 	"github.com/dtoro/oikos/internal/safego"
 	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
 )
 
 func main() {
@@ -165,6 +167,147 @@ func sseEvent(w http.ResponseWriter, flusher http.Flusher, event agentEvent) {
 	flusher.Flush()
 }
 
+// runChatTurn is the shared core of an operator-initiated turn: insert an
+// assistant placeholder, run a.chat with incremental persistence (so whatever
+// happened before an abort is never lost), finalize the row, and derive a
+// title. It is agnostic to the transport: `sink` receives every agent event
+// for delivery (SSE for a live handleChat, a no-op for a queued turn that has
+// no client attached — the frontend learns about those via the poller + the
+// status-driven "working" signal). The caller MUST already hold the session's
+// turn-gate permit.
+func (a *agent) runChatTurn(pctx, ctx context.Context, sessionID, message string, sink func(agentEvent)) {
+	toolCalls := []map[string]any{}
+	// P3: accumulate per-iteration reasoning instead of overwriting with the
+	// final `text` event (see the original inline comment in handleChat).
+	var textParts []string
+	var thinkingParts []string
+	var finalText string
+	var finalThinking string
+
+	placeholder, _ := json.Marshal(map[string]any{"role": "assistant", "text": ""})
+	msgID, err := a.store.insertMessageReturningID(pctx, sessionID, "assistant", placeholder)
+	if err != nil {
+		slog.Error("nomos: chat placeholder insert failed", "session", sessionID, "error", err)
+	}
+	persist := func() {
+		if msgID == uuid.Nil {
+			return
+		}
+		body, _ := json.Marshal(map[string]any{
+			"role":       "assistant",
+			"text":       finalText,
+			"thinking":   finalThinking,
+			"tool_calls": toolCalls,
+		})
+		a.store.updateMessage(pctx, msgID, body)
+	}
+
+	a.chat(ctx, sessionID, message, func(ev agentEvent) {
+		if ev.Type == "tool_use" || ev.Type == "tool_result" {
+			if m, ok := ev.Data.(map[string]any); ok {
+				m["type"] = ev.Type
+				// One entry per tool call: tool_use creates it, tool_result
+				// merges the result into the same entry (matched by id).
+				id, _ := m["id"].(string)
+				if id != "" && ev.Type == "tool_result" {
+					for _, existing := range toolCalls {
+						if eID, _ := existing["id"].(string); eID == id {
+							for k, v := range m {
+								existing[k] = v
+							}
+							break
+						}
+					}
+				} else {
+					toolCalls = append(toolCalls, m)
+				}
+			}
+			persist() // live: survives even if the client disconnects right after
+		}
+		if ev.Type == "text" {
+			if t, ok := ev.Data.(string); ok && t != "" {
+				if ev.IsThinking {
+					thinkingParts = append(thinkingParts, t)
+					finalThinking = strings.Join(thinkingParts, "\n\n")
+				} else {
+					textParts = append(textParts, t)
+					finalText = strings.Join(textParts, "\n\n")
+				}
+				persist()
+			}
+		}
+		sink(ev)
+	})
+
+	// B.6: if the turn ended with no text and no tool calls (the model
+	// empty-response'd and all retries failed), delete the placeholder row
+	// instead of persisting an empty bubble.
+	if finalText == "" && len(toolCalls) == 0 && msgID != uuid.Nil {
+		a.store.deleteMessage(pctx, msgID)
+	} else {
+		persist() // final state — same row, updated one last time
+	}
+
+	// Title: prefer the goal once set; else the first assistant answer.
+	if finalText != "" && sessionID != "ephemeral" {
+		var goalTitle string
+		if sess, gerr := a.store.getSession(pctx, sessionID); gerr == nil && sess.Goal != "" {
+			goalTitle = truncate(sess.Goal, 120)
+		}
+		title := goalTitle
+		if title == "" {
+			title = truncate(finalText, 80)
+		}
+		if title != "" {
+			a.store.updateSessionTitle(pctx, sessionID, title)
+		}
+	}
+}
+
+// drainAcquireWait is how long drainQueued blocks for a busy gate before
+// re-queuing and deferring to the holder's own release-drain. A package var so
+// tests can shorten it; in production it just needs to outlast the brief
+// release→drain handoff window.
+var drainAcquireWait = 5 * time.Second
+
+// drainQueued runs every queued operator message for a session as its own turn,
+// one at a time, under the turn gate. Called (in a goroutine) whenever a turn
+// releases the gate — from handleChat (live) and resumeSession (background) —
+// so a message queued while the agent was busy is acted on as soon as it's
+// free, without the operator re-sending. See messagequeue.go (plan 2026-08-03
+// F2).
+//
+// Each queued turn is persisted incrementally and has no SSE client (the
+// browser detached after receiving the `queued` event); the frontend sees the
+// result via the 3s poller and the status-driven "working" indicator.
+func (a *agent) drainQueued(ctx context.Context, sessionID string) {
+	for {
+		msg, ok := a.queue.dequeue(sessionID)
+		if !ok {
+			return
+		}
+		// Block briefly for the gate. If a live turn grabbed it first, put the
+		// message back — that turn's release will drain it again. Never stack.
+		if !a.gate.acquire(sessionID, drainAcquireWait) {
+			a.queue.requeueFront(sessionID, msg)
+			return
+		}
+		slog.Info("nomos: running queued operator message", "session", sessionID)
+		pctx := context.Background()
+		// Run the turn inside a per-iteration closure so the gate release is
+		// deferred to the end of THIS turn (and runs even if runChatTurn
+		// panics — safego recovers the panic at the goroutine boundary, so a
+		// non-deferred release would be skipped and the session's permit held
+		// forever, deadlocking all future turns). A bare `defer release` in
+		// the loop would be wrong too: Go defers run at function exit, not
+		// iteration exit, so the gate would stay held across iterations.
+		func() {
+			defer a.gate.release(sessionID)
+			a.runChatTurn(pctx, ctx, sessionID, msg, func(agentEvent) {})
+		}()
+	}
+}
+
 func handleChat(w http.ResponseWriter, r *http.Request, a *agent, st *store) {
 	if r.Method != http.MethodPost {
 		http.Error(w, "method not allowed", 405)
@@ -184,12 +327,22 @@ func handleChat(w http.ResponseWriter, r *http.Request, a *agent, st *store) {
 		return
 	}
 
-	// Empty message with an existing session = reconnect/resume. The
-	// frontend sends this after a dropped SSE stream to re-establish the
-	// connection and catch up on any auto-continuation work that happened
-	// while disconnected. Route into resumeSession so the agent sees a
-	// system note and reports current state.
+	// Empty message with an existing session = reconnect/resume. This path is
+	// defensive now — the frontend (post F2) recovers a dropped SSE via the
+	// poller + terminal task.status clearing, and no longer POSTs empty
+	// messages. If a client ever does, route into resumeSession so the agent
+	// reports current state — but SKIP a terminal session (done/failed/
+	// abandoned): there's nothing to resume, and running a "report state"
+	// turn there is just a spare turn the operator never asked for (P2.1).
 	if req.Message == "" && req.SessionID != "" {
+		if sess, err := st.getSession(context.Background(), req.SessionID); err == nil {
+			switch sess.Status {
+			case "done", "failed", "abandoned":
+				slog.Info("nomos: reconnect skipped — session already terminal", "session", req.SessionID, "status", sess.Status)
+				w.WriteHeader(202)
+				return
+			}
+		}
 		slog.Info("nomos: reconnect", "session", req.SessionID)
 		safego.Go("nomos:reconnect:"+req.SessionID, func() {
 			base := "[System: the operator's connection was re-established. The task may have progressed in the background.]"
@@ -198,7 +351,7 @@ func handleChat(w http.ResponseWriter, r *http.Request, a *agent, st *store) {
 		})
 		// Return 202 so the frontend doesn't try to consume an SSE stream
 		// from this POST — resumeSession writes to the DB directly and
-		// the poller (already running from handleDisconnect) picks it up.
+		// the poller picks it up.
 		w.WriteHeader(202)
 		return
 	}
@@ -212,8 +365,20 @@ func handleChat(w http.ResponseWriter, r *http.Request, a *agent, st *store) {
 	w.Header().Set("Content-Type", "text/event-stream")
 	w.Header().Set("Cache-Control", "no-cache")
 	w.Header().Set("Connection", "keep-alive")
+	w.Header().Set("X-Accel-Buffering", "no") // disable proxy buffering
 	w.WriteHeader(200)
 
+	// All writes to w (events + the keepalive comment below) go through one
+	// mutex: http.ResponseWriter is NOT safe for concurrent use, and the
+	// keepalive ticker runs alongside the turn's event sink (plan 2026-08-03
+	// F3). Without this, interleaved writes corrupt the SSE stream.
+	var writeMu sync.Mutex
+	writeEvent := func(ev agentEvent) {
+		writeMu.Lock()
+		defer writeMu.Unlock()
+		sseEvent(w, flusher, ev)
+	}
+
 	ctx := r.Context()
 	sessionID := req.SessionID
 
@@ -265,98 +430,65 @@ func handleChat(w http.ResponseWriter, r *http.Request, a *agent, st *store) {
 		st.answerQuestion(pctx, sessionID, qid, req.Message)
 	}
 
-	sseEvent(w, flusher, agentEvent{Type: "session", Data: sessionID, SessionID: sessionID})
+	writeEvent(agentEvent{Type: "session", Data: sessionID, SessionID: sessionID})
 
-	toolCalls := []map[string]any{}
-	// P3: accumulate per-iteration reasoning instead of overwriting with
-	// the final `text` event. The agent loop emits a `text` event for each
-	// LLM iteration that produced text (intermediate reasoning before tool
-	// calls + the final answer). Without accumulation, only the last `text`
-	// survives in the persisted row — a reload shows the final summary but
-	// not the thinking that led to each tool call.
-	var textParts []string
-	var finalText string
-
-	// Incremental persistence, mirroring resumeSession's existing
-	// placeholder+update pattern (continue.go): insert a placeholder now,
-	// update the SAME row after every tool call, so whatever happened before
-	// an abort is never lost — only what hadn't happened yet is.
-	placeholder, _ := json.Marshal(map[string]any{"role": "assistant", "text": ""})
-	msgID, err := st.insertMessageReturningID(pctx, sessionID, "assistant", placeholder)
-	if err != nil {
-		slog.Error("nomos: chat placeholder insert failed", "session", sessionID, "error", err)
-	}
-	persist := func() {
-		if msgID == uuid.Nil {
-			return
-		}
-		body, _ := json.Marshal(map[string]any{
-			"role":       "assistant",
-			"text":       finalText,
-			"tool_calls": toolCalls,
-		})
-		st.updateMessage(pctx, msgID, body)
+	// F1/F2 (plan 2026-08-03): serialize turns per session. The user message is
+	// already persisted above, so it is never lost. Wait briefly for a finishing
+	// background turn; if one is still running after that, QUEUE this message
+	// (don't reject it) and tell the client so it shows a "queued" state. The
+	// in-flight turn's release drains the queue (drainQueued) and runs it as a
+	// real turn server-side. This never stacks concurrent turns — the gate still
+	// guarantees one in-flight turn per session.
+	const turnWait = 5 * time.Second
+	if !a.gate.acquire(sessionID, turnWait) {
+		a.queue.enqueue(sessionID, req.Message)
+		slog.Info("nomos: turn already active, queued operator message", "session", sessionID)
+		writeEvent(agentEvent{Type: "queued", Data: sessionID, SessionID: sessionID})
+		writeEvent(agentEvent{Type: "done", Data: map[string]any{
+			"session_id": sessionID,
+			"queued":     true,
+		}, SessionID: sessionID})
+		return
 	}
+	defer func() {
+		a.gate.release(sessionID)
+		// Run any message that was queued while this turn held the gate. In a
+		// goroutine so the HTTP response finishes without waiting on the next
+		// turn; the queued turn has no SSE client of its own.
+		safego.Go("nomos:drain:"+sessionID, func() { a.drainQueued(context.Background(), sessionID) })
+	}()
 
-	a.chat(ctx, sessionID, req.Message, func(ev agentEvent) {
-		if ev.Type == "tool_use" || ev.Type == "tool_result" {
-			if m, ok := ev.Data.(map[string]any); ok {
-				m["type"] = ev.Type
-				// One entry per tool call: tool_use creates it, tool_result
-				// merges the result into the same entry (matched by id).
-				// Before this fix, both events appended separate entries,
-				// doubling every tool call in the persisted transcript
-				// (confirmed pre-existing in d9cdcee1, v0.3.x era).
-				id, _ := m["id"].(string)
-				if id != "" && ev.Type == "tool_result" {
-					for _, existing := range toolCalls {
-						if eID, _ := existing["id"].(string); eID == id {
-							for k, v := range m {
-								existing[k] = v
-							}
-							break
-						}
-					}
-				} else {
-					toolCalls = append(toolCalls, m)
-				}
-			}
-			persist() // live: survives even if the client disconnects right after
-		}
-		if ev.Type == "text" {
-			// P3: accumulate. Each `text` event is one iteration's reasoning
-			// (or the final answer). Join with newlines so the persisted row
-			// reads as the full transcript of what the agent said, not just
-			// the last thing.
-			if t, ok := ev.Data.(string); ok && t != "" {
-				textParts = append(textParts, t)
-				finalText = strings.Join(textParts, "\n\n")
-				persist()
+	// F3 (plan 2026-08-03): keep the SSE alive during long turns. A turn can
+	// run for many minutes (provisioning chains, deep research); the model
+	// often takes 20-40s between tool iterations, and with nothing flushed in
+	// that gap a proxy/browser idle timeout silently closes the stream. The
+	// client then sees streaming=false while the server keeps working — the
+	// "I can't tell it's working" desync. An SSE comment line (":keepalive") is
+	// ignored by EventSource but resets idle timers.
+	keepDone := make(chan struct{})
+	go func() {
+		t := time.NewTicker(12 * time.Second)
+		defer t.Stop()
+		for {
+			select {
+			case <-keepDone:
+				return
+			case <-t.C:
+				writeMu.Lock()
+				fmt.Fprintf(w, ":keepalive\n\n")
+				flusher.Flush()
+				writeMu.Unlock()
 			}
 		}
-		sseEvent(w, flusher, ev)
+	}()
+	// Defer the close (not a statement after runChatTurn) so the goroutine
+	// exits even if runChatTurn panics — net/http recovers handler panics, so
+	// a non-deferred close would be skipped and the ticker would keep writing
+	// to a dead ResponseWriter forever.
+	defer close(keepDone)
+	a.runChatTurn(pctx, ctx, sessionID, req.Message, func(ev agentEvent) {
+		writeEvent(ev)
 	})
-
-	// B.6: if the turn ended with no text and no tool calls (the model
-	// empty-response'd and all retries failed), delete the placeholder row
-	// instead of persisting an empty bubble. The error event was already
-	// streamed to the frontend via the 'done with error=true' event, so the
-	// operator sees the error inline — an empty assistant bubble in the
-	// transcript adds nothing and looks like the agent is broken.
-	if finalText == "" && len(toolCalls) == 0 && msgID != uuid.Nil {
-		st.deleteMessage(pctx, msgID)
-	} else {
-		persist() // final state — same row, updated one last time with the concluding text
-	}
-
-	// Generate a meaningful title from the assistant's first answer
-	// instead of reusing the raw user message for every session.
-	if finalText != "" && sessionID != "ephemeral" {
-		title := truncate(finalText, 80)
-		if title != "" {
-			st.updateSessionTitle(pctx, sessionID, title)
-		}
-	}
 }
 
 func handleSessionsList(w http.ResponseWriter, r *http.Request, st *store) {
@@ -370,13 +502,56 @@ func handleSessionsList(w http.ResponseWriter, r *http.Request, st *store) {
 		return
 	}
 
-	sessions, err := st.listSessions(r.Context())
+	// P2.8 (2026-07-20): filtering + pagination. The audit script in
+	// .agents/skills/session-review/SKILL.md slices `.sessions[:10]`
+	// client-side; "show me partial sessions touching lxc:rclone"
+	// required fetching the full list and filtering in JS. Push the
+	// filters into SQL so the audit becomes a single `curl | jq`.
+	// Supported query params (all optional, composable):
+	//   ?outcome=partial|success|failure       — exact match on outcome
+	//   ?status=active|done|failed|executing   — exact match on status
+	//   ?entity_id=<uuid>                      — exact match on entity_id
+	//   ?since=<RFC3339 or duration>           — last_active_at >= ...
+	//   ?blocker=<reason>                      — exact match on blocker
+	//   ?limit=<int>                           — default 50, max 200
+	//   ?cursor=<iso timestamp>                — last_active_at < cursor (page back)
+	q := r.URL.Query()
+	limit := 50
+	if v := q.Get("limit"); v != "" {
+		if n, err := strconv.Atoi(v); err == nil && n > 0 && n <= 200 {
+			limit = n
+		}
+	}
+	sessions, err := st.listSessionsFiltered(r.Context(), listFilter{
+		Outcome:  q.Get("outcome"),
+		Status:   q.Get("status"),
+		EntityID: q.Get("entity_id"),
+		Blocker:  q.Get("blocker"),
+		Since:    q.Get("since"),
+		Cursor:   q.Get("cursor"),
+		Limit:    limit,
+	})
 	if err != nil {
 		http.Error(w, err.Error(), 500)
 		return
 	}
+	// Next-page cursor: the oldest last_active_at in this page. The next
+	// request passes it as ?cursor=... to get the page before it. Empty
+	// when the list is exhausted.
+	var nextCursor string
+	if len(sessions) > 0 {
+		oldest := sessions[len(sessions)-1].LastActiveAt
+		nextCursor = oldest.UTC().Format(time.RFC3339Nano)
+		if len(sessions) < limit {
+			nextCursor = "" // last page
+		}
+	}
 	w.Header().Set("Content-Type", "application/json")
-	json.NewEncoder(w).Encode(map[string]any{"sessions": sessions})
+	json.NewEncoder(w).Encode(map[string]any{
+		"sessions":    sessions,
+		"next_cursor": nextCursor,
+		"limit":       limit,
+	})
 }
 
 func handleSessionDetail(w http.ResponseWriter, r *http.Request, st *store, a *agent) {
@@ -416,10 +591,16 @@ func handleSessionDetail(w http.ResponseWriter, r *http.Request, st *store, a *a
 	// GET /sessions/{id}/plan and /sessions/{id}/questions — REST hydration for
 	// the context panel when it first opens a task; live events carry deltas
 	// from there.
+	// GET /sessions/{id}/tool_calls — flat view of every tool call in the
+	// session, without the two-level message-shell nesting. The audit at
+	// plans/2026-07-20-session-review-ten-sessions.md P2.10 had to write
+	// Python to walk messages[].content.tool_calls[]; this endpoint makes
+	// it a single `curl | jq`.
 	if len(parts) == 2 && r.Method == http.MethodGet {
 		switch parts[1] {
 		case "plan":
-			steps, err := st.getPlanSteps(r.Context(), id)
+			all := r.URL.Query().Has("all") && r.URL.Query().Get("all") != "0" && r.URL.Query().Get("all") != "false"
+			steps, err := st.getPlanSteps(r.Context(), id, all)
 			if err != nil {
 				http.Error(w, err.Error(), 500)
 				return
@@ -436,6 +617,15 @@ func handleSessionDetail(w http.ResponseWriter, r *http.Request, st *store, a *a
 			w.Header().Set("Content-Type", "application/json")
 			json.NewEncoder(w).Encode(map[string]any{"questions": questions})
 			return
+		case "tool_calls":
+			calls, err := st.getSessionToolCalls(r.Context(), id)
+			if err != nil {
+				http.Error(w, err.Error(), 500)
+				return
+			}
+			w.Header().Set("Content-Type", "application/json")
+			json.NewEncoder(w).Encode(map[string]any{"session_id": id, "tool_calls": calls})
+			return
 		}
 	}
 
@@ -448,13 +638,36 @@ func handleSessionDetail(w http.ResponseWriter, r *http.Request, st *store, a *a
 		w.WriteHeader(204)
 
 	case http.MethodGet:
+		// P2.7 (2026-07-20): return BOTH session metadata and messages
+		// from GET /sessions/{id}. Previously this endpoint returned only
+		// {session_id, messages} — the operator had to merge with the
+		// /sessions list view to get title/goal/outcome. The eval harness
+		// at cmd/nomos/eval/main.go:302-303 already carries a comment
+		// about this leaky abstraction. The session field carries the
+		// full metadata: title, goal, outcome, summary, blocker,
+		// pending_approvals, message_count, tool_call_count, etc. The
+		// messages field is unchanged. Clients that only read
+		// `messages` keep working.
+		sess, err := st.getSession(r.Context(), id)
+		if err != nil {
+			if err == pgx.ErrNoRows {
+				http.Error(w, "session not found", 404)
+				return
+			}
+			http.Error(w, err.Error(), 500)
+			return
+		}
 		messages, err := st.getMessages(r.Context(), id)
 		if err != nil {
 			http.Error(w, err.Error(), 500)
 			return
 		}
 		w.Header().Set("Content-Type", "application/json")
-		json.NewEncoder(w).Encode(map[string]any{"session_id": id, "messages": messages})
+		json.NewEncoder(w).Encode(map[string]any{
+			"session_id": id,
+			"session":    sess,
+			"messages":   messages,
+		})
 
 	default:
 		http.Error(w, "method not allowed", 405)
@@ -605,7 +818,7 @@ func newMCPClient(baseURL, token string) (*mcpClient, error) {
 	c := &mcpClient{
 		baseURL: baseURL,
 		token:   token,
-		http:    &http.Client{Timeout: 30 * time.Second},
+		http:    &http.Client{Timeout: 120 * time.Second},
 	}
 
 	resp, err := c.doRequest("initialize", map[string]any{

cmd/nomos/messagequeue.go

@@ -0,0 +1,82 @@
+package main
+
+import (
+	"log/slog"
+	"sync"
+)
+
+// maxQueuedPerSession caps a session's queue. A held turn plus unbounded
+// enqueues would grow memory without limit; an operator nudging a long
+// autonomous turn realistically queues only a handful, so a generous cap is
+// pure insurance. Overflow drops the newest enqueue and logs (the message is
+// already persisted in the DB by handleChat before enqueue, so it isn't lost
+// from the transcript — it just won't auto-run).
+const maxQueuedPerSession = 20
+
+// messageQueue holds operator messages that arrived while a turn was already
+// running for a session. Plan 2026-08-03 (F2): instead of rejecting the
+// operator's message with "Nomos is still finishing a previous step… send it
+// again", the message is queued and auto-run when the in-flight turn releases
+// the session's turn-gate permit.
+//
+// The queue only schedules WHEN a turn runs, not WHETHER the message is stored
+// — handleChat persists the user message before acquiring the gate, so a queued
+// message is already in the transcript; this just makes sure a turn eventually
+// acts on it.
+//
+// Draining is strictly one-at-a-time under the turn gate (see drainQueued in
+// main.go), so this cannot stack concurrent turns — the exact hazard the gate
+// itself exists to prevent. Background resumeSession callers never touch this
+// queue; they keep their non-blocking skip.
+type messageQueue struct {
+	mu    sync.Mutex
+	queue map[string][]string
+}
+
+func newMessageQueue() *messageQueue {
+	return &messageQueue{queue: map[string][]string{}}
+}
+
+// enqueue appends a message to the back of the session's FIFO. Returns false
+// (and logs) if the session is already at maxQueuedPerSession — the caller's
+// message is already persisted in the DB, so this only skips auto-running it.
+func (q *messageQueue) enqueue(sessionID, msg string) bool {
+	q.mu.Lock()
+	defer q.mu.Unlock()
+	if len(q.queue[sessionID]) >= maxQueuedPerSession {
+		slog.Warn("nomos: message queue full; dropping auto-run for operator message", "session", sessionID, "cap", maxQueuedPerSession)
+		return false
+	}
+	q.queue[sessionID] = append(q.queue[sessionID], msg)
+	return true
+}
+
+// dequeue pops the next message from the front of the session's FIFO. Returns
+// ok=false when empty.
+func (q *messageQueue) dequeue(sessionID string) (string, bool) {
+	q.mu.Lock()
+	defer q.mu.Unlock()
+	xs := q.queue[sessionID]
+	if len(xs) == 0 {
+		return "", false
+	}
+	m := xs[0]
+	q.queue[sessionID] = xs[1:]
+	return m, true
+}
+
+// requeueFront pushes a message back to the front — used when a drainer popped
+// a message but lost the race for the gate to a live turn; that turn's own
+// release will drain it again.
+func (q *messageQueue) requeueFront(sessionID, msg string) {
+	q.mu.Lock()
+	defer q.mu.Unlock()
+	q.queue[sessionID] = append([]string{msg}, q.queue[sessionID]...)
+}
+
+// peek reports the queued depth for a session (test/diagnostic helper).
+func (q *messageQueue) peek(sessionID string) int {
+	q.mu.Lock()
+	defer q.mu.Unlock()
+	return len(q.queue[sessionID])
+}

cmd/nomos/messagequeue_test.go

@@ -0,0 +1,142 @@
+package main
+
+import (
+	"context"
+	"sync"
+	"testing"
+	"time"
+)
+
+func TestMessageQueue_FIFO(t *testing.T) {
+	q := newMessageQueue()
+	q.enqueue("s", "first")
+	q.enqueue("s", "second")
+	q.enqueue("s", "third")
+
+	want := []string{"first", "second", "third"}
+	for _, w := range want {
+		got, ok := q.dequeue("s")
+		if !ok || got != w {
+			t.Fatalf("dequeue = %q,%v want %q,true", got, ok, w)
+		}
+	}
+	if _, ok := q.dequeue("s"); ok {
+		t.Fatal("dequeue on drained queue should return ok=false")
+	}
+}
+
+func TestMessageQueue_RequeueFront(t *testing.T) {
+	q := newMessageQueue()
+	q.enqueue("s", "a")
+	q.enqueue("s", "b")
+	// Pop "a", then push it back to the front; "a" must come out before "b".
+	a, _ := q.dequeue("s")
+	q.requeueFront("s", a)
+	got, _ := q.dequeue("s")
+	if got != "a" {
+		t.Fatalf("after requeueFront, dequeue = %q want %q", got, "a")
+	}
+	got2, _ := q.dequeue("s")
+	if got2 != "b" {
+		t.Fatalf("next dequeue = %q want %q", got2, "b")
+	}
+}
+
+func TestMessageQueue_IsolatedPerSession(t *testing.T) {
+	q := newMessageQueue()
+	q.enqueue("s1", "one")
+	q.enqueue("s2", "two")
+	if got, _ := q.dequeue("s1"); got != "one" {
+		t.Fatalf("s1 = %q want one", got)
+	}
+	if got, _ := q.dequeue("s2"); got != "two" {
+		t.Fatalf("s2 = %q want two", got)
+	}
+	if q.peek("s1") != 0 || q.peek("s2") != 0 {
+		t.Fatal("both sessions should be drained")
+	}
+}
+
+func TestMessageQueue_Concurrent(t *testing.T) {
+	q := newMessageQueue()
+	const n = maxQueuedPerSession // stay under the cap so every enqueue lands
+	var wg sync.WaitGroup
+	for i := 0; i < n; i++ {
+		wg.Add(1)
+		go func(i int) {
+			defer wg.Done()
+			q.enqueue("s", "m")
+		}(i)
+	}
+	wg.Wait()
+	if q.peek("s") != n {
+		t.Fatalf("peek = %d want %d (all enqueues must be counted)", q.peek("s"), n)
+	}
+	seen := 0
+	for {
+		if _, ok := q.dequeue("s"); !ok {
+			break
+		}
+		seen++
+	}
+	if seen != n {
+		t.Fatalf("drained %d want %d", seen, n)
+	}
+}
+
+func TestMessageQueue_CapsOverflow(t *testing.T) {
+	q := newMessageQueue()
+	for i := 0; i < maxQueuedPerSession; i++ {
+		if !q.enqueue("s", "m") {
+			t.Fatalf("enqueue #%d within cap should succeed", i)
+		}
+	}
+	if q.enqueue("s", "overflow") {
+		t.Fatal("enqueue past the cap should return false (dropped)")
+	}
+	if got := q.peek("s"); got != maxQueuedPerSession {
+		t.Fatalf("peek = %d want %d (overflow must not append)", got, maxQueuedPerSession)
+	}
+}
+
+// drainQueued on an empty queue must be a no-op: it returns immediately and
+// never touches the gate (so the session stays free for the next turn).
+func TestDrainQueued_NoOpOnEmpty(t *testing.T) {
+	a := &agent{gate: newTurnGate(), queue: newMessageQueue()}
+	a.drainQueued(context.Background(), "s")
+	if !a.gate.acquire("s", 0) {
+		t.Fatal("gate should be free after a no-op drain (drain must not hold it)")
+	}
+	a.gate.release("s")
+}
+
+// With a queued message but the gate held by another turn, drainQueued must
+// re-queue the message and return WITHOUT running a turn (no store/provider → a
+// real run would panic). This is the "never stack" property: a busy gate
+// defers to the holder's own release-drain.
+func TestDrainQueued_RequeuesWhenBusy(t *testing.T) {
+	prev := drainAcquireWait
+	drainAcquireWait = 10 * time.Millisecond
+	t.Cleanup(func() { drainAcquireWait = prev })
+
+	a := &agent{gate: newTurnGate(), queue: newMessageQueue()}
+	if !a.gate.acquire("s", 0) {
+		t.Fatal("precondition: hold the gate")
+	}
+	a.queue.enqueue("s", "queued-msg")
+
+	done := make(chan struct{})
+	go func() {
+		a.drainQueued(context.Background(), "s") // must not panic; must requeue
+		close(done)
+	}()
+	select {
+	case <-done:
+	case <-time.After(time.Second):
+		t.Fatal("drainQueued did not return promptly while the gate was busy")
+	}
+	if got := a.queue.peek("s"); got != 1 {
+		t.Fatalf("message should be re-queued while busy; peek = %d want 1", got)
+	}
+	a.gate.release("s")
+}

cmd/nomos/retrycap.go

@@ -0,0 +1,170 @@
+package main
+
+import (
+	"crypto/sha256"
+	"encoding/hex"
+	"strings"
+	"sync"
+)
+
+// maxRunRetries is the per-turn cap on identical failing `run` tool calls.
+// After this many failures with the same (target, command) key, the agent
+// loop refuses to dispatch the call again and instead surfaces a directive
+// to investigate *why* (ps/strace/lsof) or escalate to the operator.
+//
+// Background: session 1e9c7691 (2026-07-18) retried the same
+// `chown :10000 /mnt/media_local && chmod 2775 …` ~20 times across direct
+// runs, SSH-hop-via-hubris, wrapping in a shell script, and bare `echo test`
+// sanity checks. Each retry piled up another zombie process on the target
+// (knfsd was holding a kernel lock on the exported directory). The agent
+// only investigated *why* after the operator explicitly asked
+// "the command just keeps running?" — see
+// plans/2026-07-18-session-review-three-sessions.md P0.1.
+const maxRunRetries = 3
+
+// runRetryTracker deduplicates failing `run` calls within a single chat
+// turn (chatWith invocation). It is NOT persisted across turns — the cap
+// is per-turn, so a fresh turn after the operator responds can retry once
+// more. The intent is to break a tight retry loop within one turn, not to
+// permanently block the agent from ever attempting the operation again.
+//
+// Threading: the agent loop is single-goroutine per turn, but the tracker
+// is guarded by a mutex so future callers (e.g. concurrent tool dispatch)
+// stay safe. The mutex is uncontended on the current hot path.
+type runRetryTracker struct {
+	mu     sync.Mutex
+	counts map[string]int
+}
+
+func newRunRetryTracker() *runRetryTracker {
+	return &runRetryTracker{counts: make(map[string]int)}
+}
+
+// runFailureKey is the dedup key for "this is the same command against the
+// same target." Whitespace is collapsed so trivial reformatting
+// (newlines vs spaces, trailing whitespace) doesn't escape the cap. The
+// purpose field is intentionally NOT part of the key: the agent often
+// rephrases purpose between retries while issuing the same command.
+func runFailureKey(target, command string) string {
+	collapsed := strings.Join(strings.Fields(command), " ")
+	target = strings.TrimSpace(target)
+	h := sha256.Sum256([]byte(target + "\x00" + collapsed))
+	return hex.EncodeToString(h[:])
+}
+
+// recordFailure increments the failure count for the given key and returns
+// the new count. The caller should check `count > maxRunRetries` BEFORE
+// dispatching to decide whether to skip the call.
+func (r *runRetryTracker) recordFailure(key string) int {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+	r.counts[key]++
+	return r.counts[key]
+}
+
+// failures returns the current failure count for a key (0 if unseen).
+func (r *runRetryTracker) failures(key string) int {
+	r.mu.Lock()
+	defer r.mu.Unlock()
+	return r.counts[key]
+}
+
+// isRunFailure reports whether a `run` tool call's outcome should count
+// as a failure for retry-cap purposes. A call counts as failed when:
+//   - the dispatch itself errored (callErr != nil), OR
+//   - the result text starts with "run on <target>: ERROR" — the
+//     shape classifyAndGate/sshExec produce when SSH or the command fails.
+//
+// Approvals queued ("requires approval") do NOT count as failures: they
+// are pending operator action, not a command execution failure. A read
+// of the existing code paths (classifyAndGate in internal/mcp/server.go)
+// confirms the "ERROR" prefix is the stable failure signature for `run`.
+//
+// The resultText parameter is the MCP tool's RAW text result (not JSON-
+// re-encoded): when classifyAndGate returns a textResult like
+// "run on host:strong: ERROR ...", the MCP client unwraps it back to a
+// plain Go string (see mcpClient.callTool). The caller should pass that
+// raw string, not json.Marshal's output (which would quote-wrap it).
+func isRunFailure(toolName string, resultText string, callErr error) bool {
+	if callErr != nil {
+		return true
+	}
+	if toolName != "run" {
+		return false
+	}
+	// "run on host:strong: ERROR ..." or "run on lxc:caddy: ERROR ..."
+	// Both shapes start with "run on ".
+	if !strings.HasPrefix(resultText, "run on ") {
+		return false
+	}
+	return strings.Contains(resultText, ": ERROR")
+}
+
+// runResultText extracts the raw text from a `run` tool's result value as
+// returned by mcpClient.callTool — typically a Go string, but may also be
+// a []string (multi-content result) or other JSON-decoded shape. Returns
+// "" for shapes we don't recognize. Used by the retry-cap path so
+// isRunFailure receives the un-quoted text form (see its doc comment).
+func runResultText(result any) string {
+	switch v := result.(type) {
+	case string:
+		return v
+	case []string:
+		if len(v) > 0 {
+			return v[0]
+		}
+	case []any:
+		var b strings.Builder
+		for _, e := range v {
+			if s, ok := e.(string); ok {
+				b.WriteString(s)
+			}
+		}
+		return b.String()
+	}
+	return ""
+}
+
+// runRetryDirective is the synthetic tool result returned to the model
+// when the retry cap is hit, in place of dispatching the call again. It
+// directs the agent to investigate *why* the command keeps failing before
+// retrying, or to surface the blocker to the operator.
+func runRetryDirective(target, command string, failures int) string {
+	return "Refused: this `run` against " + target + " has failed " +
+		itoa(failures) + " times this turn — retry cap hit. The command:\n  " +
+		command + "\nis almost certainly blocked by something on the target " +
+		"(a hung process, a kernel lock, an unexported FS, a stuck SSH " +
+		"session, …) — NOT a transient gateway issue. Do NOT retry with " +
+		"different routing or quoting. Instead, BEFORE calling `run` again, " +
+		"investigate *why* the command hangs: e.g. `ps aux | grep <cmd>`, " +
+		"`lsof <path>`, `strace -f -p <pid>` or `strace -f <cmd>`, " +
+		"`mount | grep <path>`, `dmesg | tail`. If you find a structural " +
+		"blocker (e.g. a kernel lock on an exported NFS directory → " +
+		"unexport → mutate → re-export), say so to the operator and fix it " +
+		"with a different command. If you genuinely cannot diagnose, " +
+		"surface the blocker to the operator with what you've tried — do " +
+		"not just retry the same command."
+}
+
+// itoa is a tiny strconv.Itoa to keep this file dependency-free.
+func itoa(n int) string {
+	if n == 0 {
+		return "0"
+	}
+	neg := n < 0
+	if neg {
+		n = -n
+	}
+	var buf [20]byte
+	i := len(buf)
+	for n > 0 {
+		i--
+		buf[i] = byte('0' + n%10)
+		n /= 10
+	}
+	if neg {
+		i--
+		buf[i] = '-'
+	}
+	return string(buf[i:])
+}

cmd/nomos/retrycap_test.go

@@ -0,0 +1,129 @@
+package main
+
+import (
+	"strings"
+	"testing"
+)
+
+func TestRunFailureKey_StableAcrossWhitespace(t *testing.T) {
+	cases := []struct{ a, b string }{
+		{"chown :10000 /mnt/media_local && chmod 2775 /mnt/media_local",
+			"chown :10000 /mnt/media_local  &&  chmod 2775 /mnt/media_local"},
+		{"chown :10000 /mnt/media_local\n&& chmod 2775 /mnt/media_local",
+			"chown :10000 /mnt/media_local && chmod 2775 /mnt/media_local"},
+		{"chown :10000 /mnt/media_local && chmod 2775 /mnt/media_local ",
+			"  chown :10000 /mnt/media_local && chmod 2775 /mnt/media_local"},
+	}
+	for i, c := range cases {
+		ka := runFailureKey("host:strong", c.a)
+		kb := runFailureKey("host:strong", c.b)
+		if ka != kb {
+			t.Errorf("case %d: keys differ for whitespace-equivalent commands:\n  a=%q\n  b=%q", i, c.a, c.b)
+		}
+	}
+}
+
+func TestRunFailureKey_DiffersByTarget(t *testing.T) {
+	a := runFailureKey("host:strong", "echo hi")
+	b := runFailureKey("host:hubris", "echo hi")
+	if a == b {
+		t.Error("keys should differ when target differs")
+	}
+}
+
+func TestRunFailureKey_DiffersByCommand(t *testing.T) {
+	a := runFailureKey("host:strong", "echo hi")
+	b := runFailureKey("host:strong", "echo bye")
+	if a == b {
+		t.Error("keys should differ when command differs")
+	}
+}
+
+func TestRunRetryTracker_CountsAndCaps(t *testing.T) {
+	r := newRunRetryTracker()
+	key := runFailureKey("host:strong", "chown :10000 /mnt/media_local")
+	for i := 1; i <= maxRunRetries; i++ {
+		if got := r.recordFailure(key); got != i {
+			t.Errorf("recordFailure #%d = %d, want %d", i, got, i)
+		}
+	}
+	// At the cap, failures() should report maxRunRetries, and the next
+	// identical call should be refused by the agent loop (failures() >=
+	// maxRunRetries).
+	if got := r.failures(key); got != maxRunRetries {
+		t.Errorf("failures = %d, want %d", got, maxRunRetries)
+	}
+	if r.failures(key) < maxRunRetries {
+		t.Errorf("cap should be enforced at maxRunRetries=%d", maxRunRetries)
+	}
+}
+
+func TestRunRetryTracker_PerTurnIsolation(t *testing.T) {
+	// Different keys don't interfere.
+	r := newRunRetryTracker()
+	k1 := runFailureKey("host:strong", "echo a")
+	k2 := runFailureKey("host:strong", "echo b")
+	r.recordFailure(k1)
+	r.recordFailure(k1)
+	if got := r.failures(k2); got != 0 {
+		t.Errorf("k2 failures = %d, want 0 (keys are isolated)", got)
+	}
+}
+
+func TestIsRunFailure(t *testing.T) {
+	cases := []struct {
+		desc    string
+		tool    string
+		result  string
+		callErr error
+		want    bool
+	}{
+		{"run with ERROR prefix", "run", "run on host:strong: ERROR ssh: signal: killed", nil, true},
+		{"run with exit error", "run", "run on lxc:caddy: ERROR exit status 1", nil, true},
+		{"run success (read-only auto)", "run", "run on host:strong (read_only, auto): hello", nil, false},
+		{"run success (assent window)", "run", "run on host:strong (config_mutation, auto via assent window): done", nil, false},
+		{"run queued for approval", "run", "run on host:strong requires approval (risk: config_mutation) — execution 019f4930 queued. Present the command and purpose to the operator and wait; do not re-request.", nil, false},
+		{"non-run tool", "get_entity", "lxc list result", nil, false},
+		{"callErr set (dispatch failure)", "run", "", errFake{}, true},
+		{"callErr set on non-run tool", "get_entity", "some result", errFake{}, true}, // callErr trumps name
+	}
+	for i, c := range cases {
+		got := isRunFailure(c.tool, c.result, c.callErr)
+		if got != c.want {
+			t.Errorf("case %d (%s): isRunFailure = %v, want %v", i, c.desc, got, c.want)
+		}
+	}
+}
+
+type errFake struct{}
+
+func (errFake) Error() string { return "fake dispatch error" }
+
+func TestRunRetryDirective_Content(t *testing.T) {
+	d := runRetryDirective("host:strong", "chown :10000 /mnt/media_local", 3)
+	for _, want := range []string{
+		"Refused:",
+		"host:strong",
+		"3 times",
+		"retry cap hit",
+		"Do NOT retry",
+		"strace",
+		"ps aux",
+		"lsof",
+		"surface the blocker",
+	} {
+		if !strings.Contains(d, want) {
+			t.Errorf("directive missing %q; got:\n%s", want, d)
+		}
+	}
+}
+
+func TestItoa(t *testing.T) {
+	cases := map[int]string{0: "0", 1: "1", 9: "9", 10: "10", 42: "42",
+		100: "100", -1: "-1", -42: "-42"}
+	for in, want := range cases {
+		if got := itoa(in); got != want {
+			t.Errorf("itoa(%d) = %q, want %q", in, got, want)
+		}
+	}
+}

cmd/nomos/store_test.go

@@ -192,7 +192,7 @@ func TestProposePlan_RefuseInFlight(t *testing.T) {
 	}
 
 	// Mark step 1 as started.
-	if err := s.updatePlanStep(ctx, sess.ID, 1, "running", ""); err != nil {
+	if err := s.updatePlanStep(ctx, sess.ID, 1, "running", "", ""); err != nil {
 		t.Fatalf("updatePlanStep: %v", err)
 	}
 
@@ -205,7 +205,7 @@ func TestProposePlan_RefuseInFlight(t *testing.T) {
 	}
 
 	// The original step 1 must be untouched — not erased, not appended to.
-	steps, err := s.getPlanSteps(ctx, sess.ID)
+	steps, err := s.getPlanSteps(ctx, sess.ID, false)
 	if err != nil {
 		t.Fatalf("getPlanSteps: %v", err)
 	}
@@ -217,7 +217,8 @@ func TestProposePlan_RefuseInFlight(t *testing.T) {
 	}
 
 	// Third call BEFORE anything runs on a fresh session: every step is
-	// still pending, so this must REPLACE, not refuse.
+	// still pending, so this must REPLACE (mark the prior plan `replaced`),
+	// not refuse. The new plan becomes generation 2.
 	sess2, err := s.createSession(ctx, "plan replace test")
 	if err != nil {
 		t.Fatalf("createSession: %v", err)
@@ -228,15 +229,146 @@ func TestProposePlan_RefuseInFlight(t *testing.T) {
 	if _, err := s.proposePlan(ctx, sess2.ID, []planStepInput{{Title: "Revised"}}); err != nil {
 		t.Fatalf("proposePlan (revise before execution): %v", err)
 	}
-	revisedSteps, err := s.getPlanSteps(ctx, sess2.ID)
+	// Default (current generation) view: only the revised step.
+	revisedSteps, err := s.getPlanSteps(ctx, sess2.ID, false)
 	if err != nil {
 		t.Fatalf("getPlanSteps: %v", err)
 	}
 	if len(revisedSteps) != 1 || revisedSteps[0].Title != "Revised" {
-		t.Fatalf("got %+v, want a single 'Revised' step (pre-execution revise must replace, not refuse)", revisedSteps)
+		t.Fatalf("got %+v, want a single 'Revised' step (current-generation view)", revisedSteps)
 	}
-	if revisedSteps[0].Generation != 1 {
-		t.Fatalf("revised step generation = %d, want 1 (fresh-start after DELETE resets generation)", revisedSteps[0].Generation)
+	if revisedSteps[0].Seq != 1 {
+		t.Fatalf("revised step seq = %d, want 1 (seq is generation-relative, resets to 1..N)", revisedSteps[0].Seq)
+	}
+	if revisedSteps[0].Generation != 2 {
+		t.Fatalf("revised step generation = %d, want 2 (prior pending plan is replaced, not deleted, so the counter increments)", revisedSteps[0].Generation)
+	}
+	// all=true audit view: both generations, the original marked `replaced`.
+	allSteps, err := s.getPlanSteps(ctx, sess2.ID, true)
+	if err != nil {
+		t.Fatalf("getPlanSteps(all): %v", err)
+	}
+	if len(allSteps) != 2 {
+		t.Fatalf("all=true got %d steps, want 2 (Original replaced gen1 + Revised gen2)", len(allSteps))
+	}
+	if allSteps[0].Title != "Original" || allSteps[0].Status != "replaced" || allSteps[0].Generation != 1 {
+		t.Errorf("gen1 step = %+v, want Original/replaced/gen1", allSteps[0])
+	}
+	if allSteps[1].Title != "Revised" || allSteps[1].Generation != 2 || allSteps[1].Seq != 1 {
+		t.Errorf("gen2 step = %+v, want Revised/gen2/seq1", allSteps[1])
+	}
+}
+
+// TestUpdatePlanStep_GenerationRelative is the P0.1 regression proof: after a
+// re-plan, update_plan_step(seq=N) — using the 1-based number the model
+// naturally carries — must address the CURRENT generation and never resurrect
+// a superseded generation's `replaced` row. Before the fix, seq was globally
+// increasing across generations, so seq=1 after a re-plan flipped the gen-1
+// `replaced` step back to `running`/`done` while the real gen-2 work went
+// unrecorded.
+func TestUpdatePlanStep_GenerationRelative(t *testing.T) {
+	s := newTestStore(t)
+	ctx := context.Background()
+
+	sess, err := s.createSession(ctx, "gen-relative seq test")
+	if err != nil {
+		t.Fatalf("createSession: %v", err)
+	}
+	// Generation 1: two steps.
+	if _, err := s.proposePlan(ctx, sess.ID, []planStepInput{{Title: "A"}, {Title: "B"}}); err != nil {
+		t.Fatalf("proposePlan #1: %v", err)
+	}
+	// Re-plan: setGoal marks the gen-1 plan `replaced`, proposePlan starts gen 2.
+	if err := s.setGoal(ctx, sess.ID, "follow-up sub-task"); err != nil {
+		t.Fatalf("setGoal: %v", err)
+	}
+	if _, err := s.proposePlan(ctx, sess.ID, []planStepInput{{Title: "C"}, {Title: "D"}}); err != nil {
+		t.Fatalf("proposePlan #2: %v", err)
+	}
+
+	// The model addresses the new plan with 1-based seq. seq=1 must hit
+	// gen-2 "C", leaving gen-1 "A" (replaced) untouched.
+	if err := s.updatePlanStep(ctx, sess.ID, 1, "running", "", ""); err != nil {
+		t.Fatalf("updatePlanStep(seq=1, running): %v", err)
+	}
+	if err := s.updatePlanStep(ctx, sess.ID, 1, "done", "", ""); err != nil {
+		t.Fatalf("updatePlanStep(seq=1, done): %v", err)
+	}
+
+	all, err := s.getPlanSteps(ctx, sess.ID, true)
+	if err != nil {
+		t.Fatalf("getPlanSteps(all): %v", err)
+	}
+	byTitle := map[string]planStep{}
+	for _, st := range all {
+		byTitle[st.Title] = st
+	}
+	// gen-1 steps stay `replaced` — NOT resurrected to running/done.
+	if byTitle["A"].Status != "replaced" || byTitle["A"].Generation != 1 {
+		t.Errorf("A = %+v, want replaced/gen1 (a superseded row must never be touched)", byTitle["A"])
+	}
+	if byTitle["B"].Status != "replaced" || byTitle["B"].Generation != 1 {
+		t.Errorf("B = %+v, want replaced/gen1", byTitle["B"])
+	}
+	// gen-2 seq=1 advanced; seq=2 untouched.
+	if byTitle["C"].Status != "done" || byTitle["C"].Generation != 2 || byTitle["C"].Seq != 1 {
+		t.Errorf("C = %+v, want done/gen2/seq1 (the 1-based update must address the current generation)", byTitle["C"])
+	}
+	if byTitle["D"].Status != "pending" || byTitle["D"].Seq != 2 {
+		t.Errorf("D = %+v, want pending/seq2", byTitle["D"])
+	}
+
+	// Out-of-range seq must be refused (no current-gen step there).
+	if err := s.updatePlanStep(ctx, sess.ID, 99, "running", "", ""); !errors.Is(err, errPlanStepNotFound) {
+		t.Fatalf("updatePlanStep(seq=99) err = %v, want errPlanStepNotFound", err)
+	}
+}
+
+// TestCompleteTask_AutoCloseEmitsEvents is the P1.1 regression proof:
+// completeTask's bulk auto-close of in-flight steps must emit one
+// plan.step.finished event per closed step (so the live panel converges
+// instead of freezing on "running" after the task completes) and must stamp
+// started_at so no closed step is left un-timestamped (P0.1 fix 5).
+func TestCompleteTask_AutoCloseEmitsEvents(t *testing.T) {
+	s := newTestStore(t)
+	ctx := context.Background()
+
+	sess, err := s.createSession(ctx, "auto-close events test")
+	if err != nil {
+		t.Fatalf("createSession: %v", err)
+	}
+	if _, err := s.proposePlan(ctx, sess.ID, []planStepInput{{Title: "A"}, {Title: "B"}}); err != nil {
+		t.Fatalf("proposePlan: %v", err)
+	}
+	// A is running, B still pending at completion time.
+	if err := s.updatePlanStep(ctx, sess.ID, 1, "running", "", ""); err != nil {
+		t.Fatalf("updatePlanStep(1, running): %v", err)
+	}
+	if err := s.completeTask(ctx, sess.ID, "success", "done"); err != nil {
+		t.Fatalf("completeTask: %v", err)
+	}
+
+	// Every auto-closed step should now carry both a started_at and a
+	// finished_at (no NULL-started `done` step).
+	steps, err := s.getPlanSteps(ctx, sess.ID, true)
+	if err != nil {
+		t.Fatalf("getPlanSteps: %v", err)
+	}
+	for _, st := range steps {
+		if st.Status == "done" && st.StartedAt == nil {
+			t.Errorf("step %q done but started_at is NULL (P0.1 fix 5: stamp it)", st.Title)
+		}
+	}
+
+	// Exactly two plan.step.finished events — one per closed step (A and B).
+	var finished int
+	if err := s.pool.QueryRow(ctx,
+		`SELECT COUNT(*) FROM events WHERE type = 'plan.step.finished' AND correlation_id = $1`,
+		sess.ID).Scan(&finished); err != nil {
+		t.Fatalf("count events: %v", err)
+	}
+	if finished != 2 {
+		t.Fatalf("plan.step.finished events = %d, want 2 (one per auto-closed step)", finished)
 	}
 }
 
@@ -265,7 +397,7 @@ func TestHadDiscoveryAndWriteback(t *testing.T) {
 
 	// A `run` call (discovery) — should set hadDiscovery, not hadEntityWriteback.
 	agentID := uuid.New()
-	s.logActivity(ctx, agentID, sess.ID, "run", nil, "", "uptime output", 100, true, "corr-1")
+	s.logActivity(ctx, agentID, sess.ID, "run", nil, "", "uptime output", 100, true, "corr-1", 0)
 	if !s.hadDiscovery(ctx, sess.ID) {
 		t.Fatal("hadDiscovery = false after a successful run call, want true")
 	}
@@ -278,7 +410,7 @@ func TestHadDiscoveryAndWriteback(t *testing.T) {
 	if err != nil {
 		t.Fatalf("createSession: %v", err)
 	}
-	s.logActivity(ctx, agentID, sess2.ID, "run", nil, "", "ssh timeout", 100, false, "corr-2")
+	s.logActivity(ctx, agentID, sess2.ID, "run", nil, "", "ssh timeout", 100, false, "corr-2", 0)
 	if s.hadDiscovery(ctx, sess2.ID) {
 		t.Fatal("hadDiscovery = true after a failed run call, want false (no facts learned)")
 	}
@@ -288,7 +420,7 @@ func TestHadDiscoveryAndWriteback(t *testing.T) {
 	if err != nil {
 		t.Fatalf("createSession: %v", err)
 	}
-	s.logActivity(ctx, agentID, sess3.ID, "get_entity", nil, "", "entity row", 10, true, "corr-3")
+	s.logActivity(ctx, agentID, sess3.ID, "get_entity", nil, "", "entity row", 10, true, "corr-3", 0)
 	if s.hadDiscovery(ctx, sess3.ID) {
 		t.Fatal("hadDiscovery = true after get_entity, want false (DB lookups are not discovery)")
 	}
@@ -298,12 +430,12 @@ func TestHadDiscoveryAndWriteback(t *testing.T) {
 	if err != nil {
 		t.Fatalf("createSession: %v", err)
 	}
-	s.logActivity(ctx, agentID, sess4.ID, "update_entity_attributes", nil, "", "ok", 10, true, "corr-4")
+	s.logActivity(ctx, agentID, sess4.ID, "update_entity_attributes", nil, "", "ok", 10, true, "corr-4", 0)
 	if !s.hadEntityWriteback(ctx, sess4.ID) {
 		t.Fatal("hadEntityWriteback = false after update_entity_attributes, want true")
 	}
 	// And the discovery+writeback combination (the conv3 scenario).
-	s.logActivity(ctx, agentID, sess4.ID, "run", nil, "", "apt-get update output", 100, true, "corr-5")
+	s.logActivity(ctx, agentID, sess4.ID, "run", nil, "", "apt-get update output", 100, true, "corr-5", 0)
 	if !s.hadDiscovery(ctx, sess4.ID) {
 		t.Fatal("hadDiscovery = false after run+writeback, want true")
 	}
@@ -311,3 +443,69 @@ func TestHadDiscoveryAndWriteback(t *testing.T) {
 		t.Fatal("hadEntityWriteback = false after run+writeback, want true")
 	}
 }
+
+// TestSetGoal_SupersessionEvent is the store-level proof for P1.4 from
+// plans/2026-07-18-session-review-three-sessions.md: when setGoal is called
+// and a non-empty prior goal already exists with a DIFFERENT value, a
+// task.superseded event must be emitted (so the audit trail records the
+// pivot — the row's goal column will be overwritten, losing the prior intent
+// without this event). When the goal is identical OR no prior goal exists,
+// no supersession event is emitted.
+//
+// Background: session 55927f0a had two set_goal calls; the first was
+// implicitly abandoned when the operator said "lets just keep ludo-library
+// then." Without the event, the prior goal silently disappeared.
+func TestSetGoal_SupersededEvent(t *testing.T) {
+	s := newTestStore(t)
+	ctx := context.Background()
+
+	sess, err := s.createSession(ctx, "goal pivot test")
+	if err != nil {
+		t.Fatalf("createSession: %v", err)
+	}
+
+	// First set_goal — no prior, no supersession event expected.
+	if err := s.setGoal(ctx, sess.ID, "Fix sabnzbd download folder to use ludo-lvm"); err != nil {
+		t.Fatalf("setGoal #1: %v", err)
+	}
+	if n := countEvents(ctx, s, sess.ID, "task.superseded"); n != 0 {
+		t.Errorf("after first set_goal: %d task.superseded events, want 0", n)
+	}
+
+	// Second set_goal with a DIFFERENT goal — supersession event expected.
+	if err := s.setGoal(ctx, sess.ID, "Add NFS export of ludo-lvm to ZimaOS"); err != nil {
+		t.Fatalf("setGoal #2: %v", err)
+	}
+	if n := countEvents(ctx, s, sess.ID, "task.superseded"); n != 1 {
+		t.Errorf("after second set_goal with a different goal: %d task.superseded events, want 1", n)
+	}
+
+	// Third set_goal with the SAME goal as the second — no new supersession
+	// event (idempotent: same goal is a no-op, not a pivot).
+	if err := s.setGoal(ctx, sess.ID, "Add NFS export of ludo-lvm to ZimaOS"); err != nil {
+		t.Fatalf("setGoal #3: %v", err)
+	}
+	if n := countEvents(ctx, s, sess.ID, "task.superseded"); n != 1 {
+		t.Errorf("after third set_goal with same goal as second: %d task.superseded events, want 1 (no new pivot)", n)
+	}
+
+	// The session's current goal must be the latest one set.
+	got, err := s.getSession(ctx, sess.ID)
+	if err != nil {
+		t.Fatalf("getSession: %v", err)
+	}
+	if got.Goal != "Add NFS export of ludo-lvm to ZimaOS" {
+		t.Errorf("session goal = %q, want the second (latest) goal", got.Goal)
+	}
+}
+
+// countEvents counts observability events of the given type correlated to
+// the given session. Used by TestSetGoal_SupersededEvent to assert the
+// task.superseded audit-trail signal was emitted.
+func countEvents(ctx context.Context, s *store, sessionID, eventType string) int {
+	var n int
+	s.pool.QueryRow(ctx,
+		`SELECT COUNT(*) FROM events WHERE correlation_id = $1 AND type = $2`,
+		sessionID, eventType).Scan(&n)
+	return n
+}

cmd/nomos/tasks.go

@@ -5,7 +5,9 @@ import (
 	"errors"
 	"fmt"
 	"log/slog"
+	"regexp"
 	"strings"
+	"time"
 )
 
 // Task tools are nomos-LOCAL, not MCP tools. They are session-scoped, and the
@@ -185,7 +187,38 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 		// what the SOUL.md "approve the plan, not each step" model actually
 		// describes. set_goal records the goal + flips status to executing
 		// and nothing more.
-		return "Goal set: " + goal + ". NEXT: pre-plan with read-only tools (search_knowledge, get_entity, list_lxcs, get_relations), then propose_plan (mandatory — even read-only tasks need a one-step plan; the run handler refuses without one). After propose_plan: if all steps are read-only, execute immediately (no approval needed). If any step is config_mutation/destructive, stop and wait for operator approval.", true
+		response := "Goal set: " + goal + ". NEXT: pre-plan with read-only tools (search_knowledge, get_entity, list_lxcs, get_relations), then propose_plan (mandatory — even read-only tasks need a one-step plan; the run handler refuses without one). After propose_plan: if all steps are read-only, execute immediately (no approval needed). If any step is config_mutation/destructive, stop and wait for operator approval."
+		// P1.3 (2026-07-20): surface prior partial/failed sessions for the
+		// same problem so the agent can pick up the thread instead of
+		// rediscovering it. Three rclone sessions (a51e2086, 8acea2e3,
+		// cb8c8a4a) all bounced off the classifier because each new session
+		// started from scratch. The agent gets a hint with the prior
+		// goal + summary; if it looks related, search_knowledge or open
+		// the prior session's transcript (GET /sessions/{id}) before
+		// re-planning. See plans/2026-07-20-session-review-ten-sessions.md.
+		prior, _ := a.store.recentPartialSessions(ctx, sessionID, 24*time.Hour)
+		if len(prior) > 0 {
+			var b strings.Builder
+			b.WriteString("\n\nNOTE — recent unfinished sessions (last 24h, outcome=partial/failed):")
+			for i, p := range prior {
+				if i >= 5 {
+					b.WriteString(fmt.Sprintf("\n  ...and %d more", len(prior)-5))
+					break
+				}
+				sum := p.Summary
+				if sum == "" {
+					sum = "(no summary)"
+				}
+				if len(sum) > 200 {
+					sum = sum[:200] + "..."
+				}
+				b.WriteString(fmt.Sprintf("\n  - %s (sid %s, outcome=%s): %s",
+					p.Goal, p.ID[:8], p.Outcome, sum))
+			}
+			b.WriteString("\nIf any of these looks like the same problem, search_knowledge for the prior investigation or read it via GET /sessions/{id} before re-planning — don't rediscover what was already learned.")
+			response += b.String()
+		}
+		return response, true
 
 	case "propose_plan":
 		raw, _ := args["steps"].([]any)
@@ -213,13 +246,17 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 		// the seq-order enforcement (5.6) require it to be completed last,
 		// and D.1's complete_task gate enforces the actual calls. Together
 		// they close the loop structurally — neither relies on the agent
-		// reading SOUL.md.
+		// reading SOUL.md. The match is broadened past the literal tool
+		// names so a natural-language step ("Write back: update entity
+		// attributes…") isn't doubled by an auto-appended duplicate (P1.2).
 		hasWritebackStep := false
 		for _, st := range steps {
-			if strings.Contains(st.Title, "update_entity_attributes") ||
-				strings.Contains(st.Title, "create_relationship") ||
-				strings.Contains(st.Detail, "update_entity_attributes") ||
-				strings.Contains(st.Detail, "create_relationship") {
+			t := strings.ToLower(st.Title + " " + st.Detail)
+			if strings.Contains(t, "update_entity_attributes") ||
+				strings.Contains(t, "create_relationship") ||
+				strings.Contains(t, "upsert_knowledge") ||
+				strings.Contains(t, "write back") ||
+				strings.Contains(t, "writeback") {
 				hasWritebackStep = true
 				break
 			}
@@ -248,8 +285,19 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 		// The writeback step is now always present (D.2 auto-appends it if
 		// the agent forgot), so the old advisory nudge is replaced by the
 		// structural gate: D.1 refuses complete_task without the actual
-		// update_entity_attributes/create_relationship calls.
-		result := fmt.Sprintf("Plan set (%d steps)%s. If all steps are read-only, execute now — call update_plan_step(running) + run for each step, no approval needed. If any step is config_mutation/destructive, STOP and wait for operator approval (\"approved\", \"yes\", \"go\", \"proceed\", \"continue\", \"ok\", \"go ahead\"). Do not call propose_plan again.", len(persisted), appendedNote)
+		// update_entity_attributes/create_relationship calls. Enumerate the
+		// step seqs so the model knows exactly which numbers to address with
+		// update_plan_step (seq is 1-based within this plan — the addressing
+		// key, not a global counter).
+		var seqs strings.Builder
+		for i, p := range persisted {
+			if i > 0 {
+				seqs.WriteString("; ")
+			}
+			title := fmt.Sprint(p["title"])
+			fmt.Fprintf(&seqs, "%v=%s", p["seq"], title)
+		}
+		result := fmt.Sprintf("Plan set (%d steps): %s.%s Address them with update_plan_step(seq=N). If all steps are read-only, execute now — call update_plan_step(running) + run for each step, no approval needed. If any step is config_mutation/destructive, STOP and wait for operator approval (\"approved\", \"yes\", \"go\", \"proceed\", \"continue\", \"ok\", \"go ahead\"). Do not call propose_plan again.", len(persisted), seqs.String(), appendedNote)
 		return result, true
 
 	case "update_plan_step":
@@ -259,7 +307,17 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 		if seq <= 0 || status == "" {
 			return "error: update_plan_step needs seq (>=1) and status", true
 		}
-		if err := a.store.updatePlanStep(ctx, sessionID, seq, status, execID); err != nil {
+		reason, _ := args["replaced_reason"].(string)
+		if err := a.store.updatePlanStep(ctx, sessionID, seq, status, execID, reason); err != nil {
+			if errors.Is(err, errPlanStepNotFound) {
+				// The seq doesn't address a step in the CURRENT plan — most
+				// often a stale 1-based number the model carried across a
+				// re-plan, or an out-of-range seq. seq is generation-relative
+				// (1..N within the latest propose_plan), so a superseded
+				// generation's row is never touched (P0.1 fix 3). Direct the
+				// model instead of silently no-op'ing.
+				return fmt.Sprintf("Step %d is not in the current plan. seq is 1-based within your latest propose_plan (a re-plan resets it to 1..N, so an old step number no longer applies). The plan was not changed. Re-address with the correct 1-based seq, or if you've lost track, re-read the plan.", seq), true
+			}
 			return fmt.Sprintf("error updating step %d: %v", seq, err), true
 		}
 		return fmt.Sprintf("Step %d → %s. (Advance with update_plan_step + run; do not re-propose.)", seq, status), true
@@ -317,6 +375,18 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 		if outcome == "success" && a.store.hadDiscovery(ctx, sessionID) && !a.store.hadEntityWriteback(ctx, sessionID) {
 			return "Refused: this session ran `run` against live targets (discovery) but did not call update_entity_attributes or create_relationship to persist what you learned. The knowledge graph will drift if you complete without writeback. Call update_entity_attributes for each entity you ran against (versions, states, counts, timestamps), and create_relationship for any edge you discovered, then call complete_task again. Outcome is held at 'executing' until you do.", true
 		}
+		// D.2: refuse success when the goal mentions a reachability/uptime
+		// check but no verification was done. The agent can't claim "X is
+		// reachable" based on a shell command alone — the proxy (Caddy) can
+		// return 200 for a terminal page (ttyd) or fallback while the actual
+		// dashboard is still down. Must call ping_service or run a successful
+		// curl before claiming success.
+		if outcome == "success" && a.store.hadDiscovery(ctx, sessionID) {
+			goal := a.store.sessionGoal(ctx, sessionID)
+			if mentionsReachability(goal) && !a.store.hadRecentVerification(ctx, sessionID) {
+				return "Refused: the goal involves a reachability or uptime check (\"make X reachable\", \"get X up\", etc.), but no ping_service call or successful curl/HTTP request against the target was detected. Caddy can return 200 for a terminal or fallback page while the actual service is still down — you must verify the service itself, not just the proxy. Call ping_service(target) or run a curl against the actual service URL, then call complete_task again. Outcome held until verified.", true
+			}
+		}
 		if err := a.store.completeTask(ctx, sessionID, outcome, summary); err != nil {
 			if errors.Is(err, errTaskAlreadyComplete) {
 				return "Task is already complete. Do not call complete_task again. If the operator pointed out a UI/sidebar inconsistency, fix it with update_plan_step (reconcile step states) or summarize the panel in your reply — do not re-execute the work.", true
@@ -333,6 +403,28 @@ func (a *agent) handleTaskTool(ctx context.Context, sessionID, name string, args
 	}
 }
 
+// reachabilityPatterns matches goal text that involves making something
+// reachable/accessible/working. Used by complete_task to surface a soft
+// warning when the session goal was about reachability but no verification
+// occurred before marking success.
+var reachabilityPatterns = []*regexp.Regexp{
+	regexp.MustCompile(`(?i)https?://[^\s]+`),
+	regexp.MustCompile(`(?i)\.hubris\.net\w+`),
+	regexp.MustCompile(`(?i)(un)?reachable`),
+	regexp.MustCompile(`(?i)(not?\s+)?(accessible|reachable|responding|resolving)`),
+	regexp.MustCompile(`(?i)diagnose\s+why`),
+	regexp.MustCompile(`(?i)(fix|restore|bring\s+back).*(accessible|reachable|online)`),
+}
+
+func mentionsReachability(goal string) bool {
+	for _, p := range reachabilityPatterns {
+		if p.MatchString(goal) {
+			return true
+		}
+	}
+	return false
+}
+
 // autoCompleteTrivialTask is the case-1 fix from
 // plans/2026-07-11-task-completion-safety-net.md: a session that never
 // called set_goal never framed itself as a structured task, so a turn that

cmd/nomos/turngate.go

@@ -0,0 +1,90 @@
+package main
+
+import (
+	"sync"
+	"time"
+)
+
+// turnGate enforces at most one in-flight agent turn per session.
+//
+// Why this exists (plan 2026-08-03, F1): handleChat runs a turn in the HTTP
+// request goroutine, and every "resume" path (the empty-message reconnect,
+// the auto-continuation worker, the idle sweep, answer-question, the /resume
+// endpoint) launches ANOTHER goroutine running a full turn. Nothing prevented
+// two turns for the SAME session at once, so a network blip that triggered a
+// reconnect would spawn a duplicate resumeSession while the original turn was
+// still alive — their tool calls interleaved on the wire and in the persisted
+// transcript, which is the root cause behind the "parallel/nesting/sequence
+// is off" and "task didn't end / flaky" reports.
+//
+// Model: one permit (buffered-1 channel seeded with a single token) per
+// session id. Acquiring consumes the token; releasing puts it back.
+//   - Background/best-effort callers (resumeSession and everything it backs)
+//     use a non-blocking acquire and SKIP when busy — a duplicate nudge while a
+//     turn is already running adds nothing, and the continuation/idle tickers
+//     will retry on their own.
+//   - The live chat path (an operator message) waits briefly for a finishing
+//     background turn, then bails with an actionable error if still busy — see
+//     handleChat.
+//
+// The permits map grows one entry per session id seen. For this single-agent
+// homelab process that set is small and bounded by real sessions; cleanup is
+// intentionally omitted (a sweep would race with acquire/release and the
+// memory is negligible).
+type turnGate struct {
+	mu      sync.Mutex
+	permits map[string]chan struct{}
+}
+
+func newTurnGate() *turnGate {
+	return &turnGate{permits: make(map[string]chan struct{})}
+}
+
+// permit returns the single token-channel for sessionID, creating and seeding
+// it on first use. Creation is guarded so two concurrent first-callers for the
+// same id share one channel.
+func (g *turnGate) permit(sessionID string) chan struct{} {
+	g.mu.Lock()
+	defer g.mu.Unlock()
+	ch, ok := g.permits[sessionID]
+	if !ok {
+		ch = make(chan struct{}, 1)
+		ch <- struct{}{}
+		g.permits[sessionID] = ch
+	}
+	return ch
+}
+
+// acquire takes the session's permit. With wait <= 0 it is non-blocking
+// (returns false immediately if a turn is active). With wait > 0 it blocks up
+// to wait for the permit, returning false on timeout. Every true return MUST
+// be paired with exactly one release.
+func (g *turnGate) acquire(sessionID string, wait time.Duration) bool {
+	ch := g.permit(sessionID)
+	if wait <= 0 {
+		select {
+		case <-ch:
+			return true
+		default:
+			return false
+		}
+	}
+	t := time.NewTimer(wait)
+	defer t.Stop()
+	select {
+	case <-ch:
+		return true
+	case <-t.C:
+		return false
+	}
+}
+
+// release returns the session's permit. Idempotent: a release with no matching
+// acquire (or a double release) is a no-op rather than a blocking send.
+func (g *turnGate) release(sessionID string) {
+	ch := g.permit(sessionID)
+	select {
+	case ch <- struct{}{}:
+	default:
+	}
+}

cmd/nomos/turngate_test.go

@@ -0,0 +1,114 @@
+package main
+
+import (
+	"sync"
+	"sync/atomic"
+	"testing"
+	"time"
+)
+
+func TestTurnGate_NonBlockingSkipsWhenBusy(t *testing.T) {
+	g := newTurnGate()
+	if !g.acquire("s1", 0) {
+		t.Fatal("first non-blocking acquire should succeed on a free session")
+	}
+	// A second non-blocking acquire (a background resume) must skip, not queue.
+	if g.acquire("s1", 0) {
+		t.Fatal("second non-blocking acquire should fail while a turn is active")
+	}
+	// A different session is independent.
+	if !g.acquire("s2", 0) {
+		t.Fatal("acquire on a different session should succeed")
+	}
+	g.release("s2")
+	g.release("s1")
+	// After release, the session is free again.
+	if !g.acquire("s1", 0) {
+		t.Fatal("acquire should succeed again after release")
+	}
+	g.release("s1")
+}
+
+func TestTurnGate_BlockingAcquireWaitsForRelease(t *testing.T) {
+	g := newTurnGate()
+	if !g.acquire("s1", 0) {
+		t.Fatal("first acquire should succeed")
+	}
+
+	got := make(chan bool, 1)
+	go func() { got <- g.acquire("s1", 2*time.Second) }()
+
+	select {
+	case <-got:
+		t.Fatal("blocking acquire should wait, not return before release")
+	case <-time.After(50 * time.Millisecond):
+		// expected: still waiting
+	}
+
+	g.release("s1")
+	select {
+	case ok := <-got:
+		if !ok {
+			t.Fatal("blocking acquire should succeed after release")
+		}
+	case <-time.After(time.Second):
+		t.Fatal("blocking acquire did not return after release")
+	}
+	g.release("s1")
+}
+
+func TestTurnGate_BlockingAcquireTimesOut(t *testing.T) {
+	g := newTurnGate()
+	g.acquire("s1", 0) // hold the permit
+
+	start := time.Now()
+	if g.acquire("s1", 60*time.Millisecond) {
+		t.Fatal("acquire should time out while permit is held")
+	}
+	if elapsed := time.Since(start); elapsed < 50*time.Millisecond {
+		t.Fatalf("acquire returned too fast (%v); expected to wait ~60ms", elapsed)
+	}
+	g.release("s1")
+}
+
+// TestTurnGate_SingleFlightConcurrent is the core F1 guarantee: many concurrent
+// background acquirers on the SAME session, exactly one runs at a time. This is
+// the property that prevents two turns interleaving tool calls.
+func TestTurnGate_SingleFlightConcurrent(t *testing.T) {
+	g := newTurnGate()
+	const n = 50
+	var inFlight, maxInFlight int64
+	var runs int64
+	var wg sync.WaitGroup
+	wg.Add(n)
+	start := make(chan struct{})
+	for i := 0; i < n; i++ {
+		go func() {
+			defer wg.Done()
+			<-start
+			if !g.acquire("shared", 0) { // background-style: skip if busy
+				return
+			}
+			defer g.release("shared")
+			cur := atomic.AddInt64(&inFlight, 1)
+			for {
+				m := atomic.LoadInt64(&maxInFlight)
+				if cur <= m || atomic.CompareAndSwapInt64(&maxInFlight, m, cur) {
+					break
+				}
+			}
+			atomic.AddInt64(&runs, 1)
+			time.Sleep(2 * time.Millisecond)
+			atomic.AddInt64(&inFlight, -1)
+		}()
+	}
+	close(start)
+	wg.Wait()
+
+	if maxInFlight != 1 {
+		t.Fatalf("max in-flight turns = %d, want 1 (turns must not overlap)", maxInFlight)
+	}
+	if runs == 0 {
+		t.Fatal("expected at least one turn to run")
+	}
+}

compose/web/Caddyfile

@@ -1,5 +1,27 @@
 :80 {
 	root * /srv
-	file_server
-	try_files {path} /index.html
+
+	# /wails/runtime.js is injected by the Wails desktop wrapper, which serves
+	# the same dist/ from its own asset handler. In a browser it does not
+	# exist, and the SPA fallback below answered it with index.html — so the
+	# browser parsed "<!doctype html>" as JavaScript and threw
+	# "SyntaxError: expected expression, got '<'" on every page load.
+	# Return a real 404 instead: the tag fails quietly, and the desktop app is
+	# unaffected because it never reaches this server.
+	handle /wails/* {
+		error 404
+	}
+
+	# Same reasoning for any other asset: a missing .js/.css/.map answered with
+	# HTML is always a confusing parse error rather than an honest 404. Only
+	# real routes should fall through to the SPA.
+	@asset path_regexp \.(js|mjs|css|map|json|png|jpg|svg|ico|woff2?)$
+	handle @asset {
+		file_server
+	}
+
+	handle {
+		file_server
+		try_files {path} /index.html
+	}
 }

compose/web/Dockerfile

@@ -8,7 +8,8 @@ FROM node:22-alpine AS builder
 
 WORKDIR /build/web
 COPY web/package.json web/package-lock.json ./
-RUN npm ci
+COPY web/vendor /build/vendor
+RUN npm install --no-audit --no-fund
 COPY VERSION ./
 COPY web/ ./
 RUN npm run build

docker-compose.yml

@@ -83,6 +83,18 @@ services:
     command: ["api"]
     stop_signal: SIGTERM
     stop_grace_period: 30s
+    # Exists so nomos can wait for the API to actually answer rather than just
+    # for its container to exist — see nomos's depends_on below. wget is
+    # BusyBox's, already in the alpine runtime image, so this adds no
+    # dependency. /healthz pings the DB, so "healthy" means genuinely ready.
+    healthcheck:
+      test: ["CMD", "wget", "-q", "-O", "-", "http://127.0.0.1:8090/healthz"]
+      interval: 5s
+      timeout: 3s
+      retries: 10
+      # Migrations and seed run before this container, but the first bind can
+      # still take a moment; failures inside the start period don't count.
+      start_period: 10s
 
   # Scheduler (Phase 3) — observe loop
   scheduler:
@@ -139,7 +151,12 @@ services:
     profiles: ["full"]
     depends_on:
       api:
-        condition: service_started
+        # service_started only waits for the container to exist, so nomos came
+        # up while the API was still binding :8090, failed its MCP initialize,
+        # exited 1, and crash-looped for ~25s on every single deploy. It always
+        # recovered, which is exactly why it went unnoticed. service_healthy
+        # waits for the API to actually answer.
+        condition: service_healthy
     environment:
       NOMOS_MCP_URL: http://api:8090/mcp
       NOMOS_AGENT_SLUG: agent:nomos

docs/adr/0012-hermes-oikos-interactions.md

@@ -234,9 +234,33 @@ sequenceDiagram
 
 ---
 
-**2026-07-08 — renamed to Nomos.** The Hermes agent gateway was renamed to
+**2026-07-08 — renamed to Nomos.**
 Nomos (from *oikonomos*, the steward of the oikos) under the
 [Nomos resident agent plan](../../plans/2026-07-08-nomos-resident-agent.md),
+
+### Hermes MCP client setup
+
+To connect a Hermes Agent instance to oikos as a native MCP client, add to
+`~/.hermes/config.yaml`:
+
+```yaml
+mcp_servers:
+  oikos:
+    url: "https://mcp.hubris.network/mcp"
+    headers:
+      Authorization: "Bearer <OIKOS_MCP_BEARER_TOKEN>"
+    timeout: 180
+```
+
+Run `/reload-mcp` in-session or restart Hermes. Tools appear as
+`mcp__oikos__*`.
+
+**Caveat:** Hermes stores the bearer token in plaintext in `config.yaml` —
+it does not support `${VAR}` interpolation in MCP server headers. Ensure
+`security.redact_secrets: true` (default) so the token value is stripped
+from tool output and logs. File an upstream feature request at
+https://github.com/NousResearch/hermes-agent/issues for env-var
+interpolation support.
 N0 milestone. The gateway binary (`cmd/nomos`), Docker service, DB slug
 (`agent:nomos`), and all referencing docs were updated. All architectural
 principles in this ADR remain unchanged.

docs/index.md

@@ -0,0 +1,17 @@
+# Docs
+
+Long-form reference material for the Oikos platform. Operational state and
+topology live in the DB (seeded from `seeds/`); these docs cover decisions,
+procedures, and the system model.
+
+| Path | Contents |
+| ---- | -------- |
+| [adr/](adr/README.md) | Architecture Decision Records (numbered, append-only) |
+| [mbse/](mbse/README.md) | Model-Based Systems Engineering views of the platform |
+| [mascot/](mascot/README.md) | MBSE subsystem model for the desktop mascot (planned) |
+| [operations/](operations/README.md) | Operator runbooks (deploy, rollback, recovery) |
+
+For agent orientation see [AGENTS.md](../AGENTS.md); for the operating model
+see [.agents/OIKOS.md](../.agents/OIKOS.md); for development see
+[CONTRIBUTING.md](../CONTRIBUTING.md). Design plans live in
+[plans/](../plans/), not here.

docs/mascot/README.md

@@ -0,0 +1,371 @@
+# Oikos — Desktop Mascot Subsystem Model
+
+> Companion to [the platform Model](../mbse/README.md) and
+> [the Framework](../mbse/framework.md). This document is a **subsystem
+> Model** in Holt's sense — it conforms to the same Framework (Ontology +
+> Viewpoints, Markdown + Mermaid Notation) rather than restating it, scoped
+> to a single not-yet-built subsystem of the `web` component: the desktop
+> mascot ("Cluck"), a pixel-art chicken that lives on the desktop shell.
+> Where the platform-wide Views in [../mbse/README.md](../mbse/README.md)
+> and the component View for `web/src` in
+> [../mbse/components.md](../mbse/components.md#5-web-control-room) speak
+> at the level of "the SPA," this document goes one layer deeper into one
+> feature of it — the same relationship [components.md](../mbse/components.md)
+> has to [README.md](../mbse/README.md), applied recursively.
+
+**Status of this Model:** the subsystem it describes is **implemented**
+in `web/src/lib/mascot/` and `web/public/mascot/` (as of 2026-07-20).
+Views below are marked **Implemented** where the code matches; a small
+number of requirements (distinct adult art, a true round radial menu)
+remain **Planned** as polish items. The corresponding implementation plan
+is [plans/2026-07-20-desktop-mascot.md](../../plans/2026-07-20-desktop-mascot.md),
+which carries a deviation note at the top covering the changes made
+during implementation (hatch-on-naming, PNG-sheet art, button-column
+radial menu, 60fps loop), and the physics audit/follow-up is
+[plans/2026-07-20-mascot-physics-audit.md](../../plans/2026-07-20-mascot-physics-audit.md).
+
+## Views in this model
+
+| # | View | Concern it addresses |
+|---|---|---|
+| [1](#1-mission--system-context) | Mission & System Context | Why a mascot, and what is it never allowed to do? |
+| [2](#2-requirements) | Requirements | What must it do, traced from the original request? |
+| [3](#3-structural-view) | Structural View | What modules make it up, and which are the extension points? |
+| [4](#4-behavioral-view) | Behavioral View | How does it move, live, and react, moment to moment? |
+| [5](#5-interfaces-view) | Interfaces View | What does it read from the rest of the system, and how does it persist itself? |
+| [6](#6-extension-guide) | Extension Guide | How does a future engineer add an animation, behavior, menu action, or reaction? |
+| [7](#7-verification-view) | Verification View | How will we know it works, once built? |
+
+## 1. Mission & System Context
+
+**Stakeholders:** the operator (delight, ambient awareness of system
+state without opening a window); future engineers extending the mascot's
+behaviors/reactions/menu.
+
+**Mission:** give the desktop shell a persistent, living presence that
+makes background system activity legible at a glance — a chat streaming,
+a knowledge-graph write, a critical signal — without requiring a window to
+be open, while doubling as a lightweight tamagotchi for its own sake
+(delight is a legitimate requirement here, not a side effect).
+
+**Boundary — what the mascot is, and is not:**
+
+- It is a **purely client-side, read-only observer**. It subscribes to
+  existing `web` stores (chat, activity, events, dashboard summary) the
+  same way any other UI component does.
+- It **never calls a mutating API endpoint** and is not a new actuation
+  path — it has no relationship to the `run` gate, `Execution`, or
+  `Approval` entities described in [the platform Ontology](../mbse/ontology.md).
+  Its only "mutation" is its own tamagotchi state, stored client-side.
+- It is scoped entirely inside the `web` component
+  ([../mbse/components.md §5](../mbse/components.md#5-web-control-room));
+  it introduces no new backend surface, no new MCP tool, no new REST route.
+
+```mermaid
+flowchart TB
+    subgraph SURFACE["Desktop shell surface (Desktop.svelte)"]
+        ICONS["Icon layer\nz-0"]
+        LAUNCH["Task launcher\nz-10"]
+        WIN["WindowLayer\nz-40"]
+        MASCOT["MascotLayer\nz-45\n(this subsystem)"]
+        MENU["Desktop context menu\nz-50"]
+    end
+
+    MASCOT -->|subscribes, read-only| EVENTS["stores/events.ts\nliveEvents (SSE)"]
+    MASCOT -->|subscribes, read-only| CHAT["stores/chat.ts\nstreaming"]
+    MASCOT -->|subscribes, read-only| ACTIVITY["stores/activity.ts\nactivityLog"]
+    MASCOT -->|subscribes, read-only| CONTEXT["stores/context.ts\nsummary"]
+    MASCOT -->|reads/writes| LS["localStorage\noikos-mascot"]
+
+    style MASCOT fill:#fff3e0,stroke:#e65100
+```
+
+## 2. Requirements
+
+Traced from the original feature request. Status reflects the
+2026-07-20 implementation; **Planned** items are deferred polish.
+
+| ID | Statement | Source | Status |
+|---|---|---|---|
+| MASC-1 | The mascot SHALL render as pixel-art from bundled 16x16 PNG sprite sheets (chicken + egg packs), not code-drawn string grids | User request (relaxed from "code-drawn" during implementation — see plan deviation note) | Implemented |
+| MASC-2 | The mascot SHALL roam the desktop surface autonomously, walking along the ground (surface bottom, above the taskbar, OR the top edge of any non-minimized window beneath it) under gravity | User request + design decision | Implemented |
+| MASC-3 | The mascot SHALL be draggable with the mouse; releasing it mid-air SHALL trigger a flutter-fall back to the ground | User request + design decision | Implemented |
+| MASC-4 | Right-clicking the mascot SHALL open an interaction menu supporting nested submenus; rendered as a rounded-button column (relaxed from "round/Sims-style" — see plan deviation note) | User request | Implemented |
+| MASC-5 | The mascot SHALL have a tamagotchi lifecycle: egg → chick → adult, with a user-assignable name; the egg → chick transition fires on first naming, not on a timed incubation | User request | Implemented |
+| MASC-6 | The mascot's stage, name, and stats SHALL persist across reloads | User request (implied by "tamagotchi") | Implemented |
+| MASC-7 | The mascot SHALL have idle states (autonomous behavior when untouched) and interactive states (drag, click, menu) | User request | Implemented |
+| MASC-8 | The mascot SHALL react visibly to real application activity: chat streaming, knowledge-graph writes, critical signals | User request ("aware of its environment... feels alive and connected") | Implemented |
+| MASC-9 | Animations, behaviors, menu actions, and reactions SHALL each be defined in a single data-driven registry, so a new one can be added without touching the engine code | User request ("easily expansible") | Implemented |
+| MASC-10 (NFR) | The mascot's game loop SHALL run via `setTimeout`, not `requestAnimationFrame`, matching the repo's existing [`GraphBackground.svelte`](../../web/src/lib/components/GraphBackground.svelte) convention (rAF suspends in some hidden-tab embeddings); runs at ~60fps (relaxed from 30fps for smoother drag/fall — see plan deviation note) | Codebase convention | Implemented |
+| MASC-11 (NFR) | The mascot SHALL never write to the API; all mutation is local (localStorage) | Design decision, this document §1 | Implemented |
+| MASC-12 (NFR) | Persistence writes SHALL be debounced (~300ms), never per animation frame | Codebase convention ([`stores/windows.ts`](../../web/src/lib/stores/windows.ts) wmkit persist) | Implemented |
+
+## 3. Structural View
+
+**Stakeholders:** an engineer implementing or extending the mascot.
+**Why this View earns its place:** MASC-9 (extensibility) is only real if
+the module boundaries actually separate data (registries) from engine
+code; this View is the check that they do.
+
+```mermaid
+classDiagram
+    class types_ts {
+        <<module>>
+        PixelGrid
+        AnimName
+        MascotStage
+        BehaviorId
+        Stimulus
+        RadialAction
+    }
+    class palette_ts {
+        <<module, registry>>
+        PALETTE: char to CSS color
+    }
+    class sprites_ts {
+        <<module, registry>>
+        SPRITES: Stage to AnimName to AnimDef
+        resolveAnim(stage, name)
+    }
+    class render_ts {
+        <<module, stateless>>
+        drawFrame(ctx, grid, palette, flip)
+    }
+    class state_svelte_ts {
+        <<module, runes>>
+        MascotModel state
+        grantXp() feed() pet() setName()
+        tickLifecycle() advanceStageIfReady()
+        persist (debounced, oikos-mascot)
+    }
+    class behavior_ts {
+        <<module, registry>>
+        BEHAVIORS: BehaviorId to BehaviorDef
+        stepMascot(rt, model, now, dt)
+    }
+    class stimuli_ts {
+        <<module, registry>>
+        REACTIONS: id to ReactionDef
+        attachStimuli(emit)
+    }
+    class actions_ts {
+        <<module, registry>>
+        MASCOT_ACTIONS: RadialAction tree
+        registerMascotAction()
+    }
+    class Mascot_svelte {
+        <<component>>
+        canvas render loop 30fps
+        pointer drag/click/contextmenu
+    }
+    class MascotLayer_svelte {
+        <<component>>
+        z-45 absolute overlay
+        hosts Mascot + RadialMenu + bubble
+    }
+    class RadialMenu_svelte {
+        <<component>>
+        z-60 fixed, nested rings
+    }
+    class NameDialog_svelte {
+        <<component>>
+    }
+
+    sprites_ts --> palette_ts : indexes
+    sprites_ts --> types_ts : uses
+    Mascot_svelte --> render_ts : draws frames
+    Mascot_svelte --> sprites_ts : resolves anim
+    Mascot_svelte --> behavior_ts : steps FSM
+    Mascot_svelte --> state_svelte_ts : reads/mutates model
+    MascotLayer_svelte --> Mascot_svelte : hosts
+    MascotLayer_svelte --> RadialMenu_svelte : hosts, on contextmenu
+    MascotLayer_svelte --> stimuli_ts : attaches on mount
+    MascotLayer_svelte --> NameDialog_svelte : hosts, on hatch/rename
+    RadialMenu_svelte --> actions_ts : renders tree
+    stimuli_ts --> behavior_ts : forceBehavior(react)
+```
+
+**The four extension registries** (MASC-9's concrete answer — see also
+[§6 Extension Guide](#6-extension-guide)): `SPRITES` (animations),
+`BEHAVIORS` (autonomous states), `MASCOT_ACTIONS` (radial menu tree),
+`REACTIONS` (environment stimuli). Each is plain data; the engine
+(`behavior.ts`'s `stepMascot`, `Mascot.svelte`'s loop, `RadialMenu.svelte`'s
+renderer) is generic over whatever the registry currently contains.
+
+**Mount point:** two lines in
+[`Desktop.svelte`](../../web/src/lib/components/desktop-shell/Desktop.svelte) —
+`<MascotLayer />` rendered inside the surface `<div>` (the `relative
+min-h-0 flex-1 overflow-hidden` element), after `<WindowLayer />`, so its
+`absolute inset-0` shares the surface's coordinate space and its ground
+line is exactly the surface's bottom edge (= the taskbar's top edge).
+
+## 4. Behavioral View
+
+**Stakeholders:** an engineer reasoning about "what does the mascot do
+right now, and why." **Why this View earns its place:** a mascot with an
+implicit, ad-hoc state machine is unmaintainable the moment a second
+behavior or reaction is added; this View is the state machine made
+explicit before any of it is coded.
+
+### 4.1 Behavior FSM (moment-to-moment autonomy)
+
+```mermaid
+stateDiagram-v2
+    [*] --> egg
+    egg --> chick : first naming submitted\n(forceHatch: hatchProgress=1)
+
+    state chick_and_adult_behaviors {
+        [*] --> idle
+        idle --> wander : weighted random pick\non behaviorUntil expiry
+        wander --> idle
+        idle --> peck : weighted random pick
+        peck --> idle
+        idle --> hop : weighted random pick
+        hop --> idle : touchdown\n(off-edge mid-hop hands to falling)
+        idle --> sleep : weighted random pick
+        sleep --> idle
+        wander --> falling : y below ground\n(off a dragged edge, etc.)
+        idle --> dragged : pointerdown + move\npast 5px threshold
+        wander --> dragged : pointerdown + move
+        sleep --> dragged : pointerdown + move\n(interrupts sleep)
+        dragged --> falling : pointerup, released mid-air\n(toss velocity from pointer history)
+        falling --> falling : hard impact\n(one diminished bounce)
+        falling --> land : y reaches ground\n(sideways momentum -> skid)
+        land --> idle
+        [*] --> react : stimulus dispatched\n(priority/cooldown gated)
+        react --> idle : durationMs elapsed,\nreturns to prior-or-idle
+    }
+
+    chick --> adult : xp reaches ADULT_XP\n(advanceStageIfReady)
+```
+
+`dragged` always wins over any autonomous behavior; `sleep` is broken only
+by a reaction whose `ReactionDef.interruptsSleep` is true (§4.3) or by a
+drag. Weighted-random idle selection (`weight` field in `BehaviorDef`)
+picks the next autonomous behavior only when the current one's `next()`
+returns null past `behaviorUntil` — see
+[plans/2026-07-20-desktop-mascot.md](../../plans/2026-07-20-desktop-mascot.md)
+for the concrete weights.
+
+**Physics feel (implemented 2026-07-20, second pass):** the fall is a
+losing attempt at flight, not a drop — wing-beat impulses on a
+speed-scaled, jittered flap cycle (panic flapping) shave the descent;
+falls faster than terminal velocity (hard downward tosses) decay back
+under drag instead of clamping; hard impacts bounce once, squash via a
+damped-spring render layer scaled by impact speed, and poof a burst of
+feather pixels; sideways momentum becomes a friction skid on touchdown
+and ricochets off the surface's side bounds mid-fall; the sprite
+stretches along its motion in the air and tilts into horizontal velocity
+(fall, drag, and skid); walking bobs at step frequency. All of it is
+tuning in `behavior.ts` plus the pure render layer in `Mascot.svelte`'s
+`updateJuice()` — no new assets, no new states beyond `hop`.
+
+### 4.2 Tamagotchi lifecycle (long-lived state)
+
+```mermaid
+stateDiagram-v2
+    [*] --> egg : first load,\ndefaultModel()
+    egg --> chick : first naming submitted\n(forceHatch sets hatchProgress=1)\n+ NameDialog shown
+    chick --> adult : xp >= ADULT_XP (200)
+    adult --> [*]
+```
+
+This is a separate state machine from §4.1: §4.1 governs frame-to-frame
+motion/animation, §4.2 governs the tamagotchi's slow-moving `MascotModel`
+(persisted, ticked ~1x/sec via `tickLifecycle`, not every frame). The
+egg → chick transition fires on first naming, not on a timed incubation
+— see the deviation note in
+[plans/2026-07-20-desktop-mascot.md](../../plans/2026-07-20-desktop-mascot.md).
+
+### 4.3 Example sequence — an environment stimulus becomes a visible reaction
+
+```mermaid
+sequenceDiagram
+    participant SSE as stores/events.ts (SSE)
+    participant Stim as stimuli.ts attachStimuli
+    participant Layer as MascotLayer.svelte (emit callback)
+    participant FSM as behavior.ts
+    participant Mascot as Mascot.svelte (canvas)
+
+    SSE->>Stim: liveEvents updates,\nnew head event severity=critical
+    Stim->>Stim: check REACTIONS['alarmed']\ncooldown + priority
+    Stim->>Layer: emit(reaction)
+    Layer->>Layer: if model.stage === 'egg': drop\n(egg isn't "alive" yet)
+    Layer->>FSM: forceBehavior(rt, 'react', {anim, durationMs})
+    FSM->>FSM: interrupts current behavior\n(even sleep, interruptsSleep=true)
+    FSM->>Mascot: rt.behavior = 'react', rt.anim = 'react-alarm'
+    Mascot->>Mascot: next ~60fps tick draws\nreact-alarm frame + bubble
+    Note over FSM: after durationMs,\nnext() returns to idle
+```
+
+**Egg-stage suppression:** MascotLayer's `emit` callback drops any
+reaction when `model.stage === 'egg'`. The egg isn't "alive" yet (no
+name, no hatched chick to react), so stimulus events are silently
+ignored until the egg hatches — this keeps the egg calm during the
+naming dialog rather than playing alarm animations behind it.
+
+## 5. Interfaces View
+
+**Stakeholders:** an engineer wiring a new store into the mascot's
+awareness, or auditing what it depends on.
+
+| Interface | Direction | Shape | Notes |
+|---|---|---|---|
+| [`stores/events.ts`](../../web/src/lib/stores/events.ts) `liveEvents` | consumed | `Writable<OikosEvent[]>`, newest-first, ref-counted via `subscribeEvents()` | `OikosEvent.type` families: `approval.*`, `signal.*`, `execution.*`, `health.changed`; `severity: 'info'\|'warning'\|'critical'` |
+| [`stores/chat.ts`](../../web/src/lib/stores/chat.ts) `streaming` | consumed | `Writable<boolean>` | false→true edge triggers the `thinking` reaction, held while true |
+| [`stores/activity.ts`](../../web/src/lib/stores/activity.ts) `activityLog` | consumed | derived `Readable<ActivityEntry[]>`, **recomputed wholesale** on every emission — not append-only | new entries with `type === 'knowledge'` detected by diffing entry `id`s between emissions, not by treating it as a stream |
+| [`stores/context.ts`](../../web/src/lib/stores/context.ts) `summary` | consumed | `Writable<DashboardSummary\|null>` | ambient state (open signal counts via `openSignalCount(summary)`) |
+| `localStorage['oikos-mascot']` | owned | `MascotModel` JSON, `{ version: 1, stage, name, hatchProgress, happiness, xp, hatchedAt, lastPos: {x}, lastSeen }` (hatchProgress is binary 0/1: 0 until first naming, 1 after) | debounced write (~300ms, mirrors [`stores/windows.ts`](../../web/src/lib/stores/windows.ts) wmkit persist) + `beforeunload` flush; `version` field reserved for a future `migrate()`; multi-tab is last-writer-wins (accepted, documented, not solved) |
+| [`Desktop.svelte`](../../web/src/lib/components/desktop-shell/Desktop.svelte) mount | owned | `<MascotLayer />`, 2-line insertion | see §3 |
+
+No interface in this table is a write path to the Oikos API — consistent
+with §1's boundary statement (MASC-11).
+
+## 6. Extension Guide
+
+**Stakeholders:** a future engineer adding one new animation, behavior,
+menu action, or reaction — this is the Viewpoint 4's "why" made concrete
+as a recipe rather than prose (mirrors [../mbse/framework.md §7](../mbse/framework.md)'s
+Process Set treatment).
+
+| To add a... | Touch only | Nothing else changes because |
+|---|---|---|
+| **Animation** | Add the name to the `AnimName` union in `types.ts`; add frames to `SPRITES[stage]` in `sprites.ts` | `resolveAnim()` and the renderer are generic over the registry |
+| **Behavior** | Add the id to `BehaviorId`; add one `BehaviorDef` entry to `BEHAVIORS` in `behavior.ts` | `stepMascot()` and the weighted-random idle selector consume `BEHAVIORS` generically |
+| **Radial menu action** | Add a `RadialAction` node to `MASCOT_ACTIONS` in `actions.ts` (or call `registerMascotAction()`), optionally nested under `children` | `RadialMenu.svelte` renders whatever tree it's given, including nesting depth |
+| **Environment reaction** | Add a `ReactionDef` to `REACTIONS` in `stimuli.ts`; wire one `store subscription -> predicate -> emit(reaction)` block inside `attachStimuli()` | priority/cooldown/interrupt dispatch logic in `attachStimuli()` is generic over `REACTIONS` |
+
+## 7. Verification View
+
+**Stakeholders:** whoever implements this subsystem and needs to know
+when it's actually done, not just compiled.
+
+Manual browser checklist (no automated test harness planned for v1 — see
+[plans/2026-07-20-desktop-mascot.md](../../plans/2026-07-20-desktop-mascot.md)
+for the same list in implementation-order context):
+
+- Egg renders grounded at the surface bottom, wiggles gently while the
+  name dialog is open, and survives a reload at the same x (confirm
+  `oikos-mascot` is debounced — no writes fire from mere walking, only
+  from discrete transitions).
+- Dragging the egg up and releasing triggers a flutter-fall with no
+  tunneling below the taskbar; dragging past the surface edges clamps.
+- A fresh egg (no name) opens the name dialog on mount; submitting it
+  hatches to chick; the name persists across reload. The debug "Force
+  hatch" action does the same without prompting.
+- Chick wanders and flips sprite at surface edges, pecks, sleeps
+  autonomously; a plain click (no drag) triggers a pet/hop reaction.
+- Right-clicking the chicken opens the radial menu centered on it, without
+  triggering the desktop's own right-click menu; a nested submenu (Feed)
+  opens correctly; Escape pops one level then closes; an outside click
+  closes it; the menu stays fully visible when the chicken is near a
+  screen edge or corner.
+- With one or more windows open (including a maximized one), the chicken
+  visibly walks above them without breaking window drag/resize/close.
+- Starting a chat and observing it stream triggers the `thinking` reaction
+  for the duration; a simulated knowledge-graph write triggers `eureka`
+  once per cooldown window; a simulated critical signal triggers `alarmed`
+  even while the chicken is asleep.
+- Resizing the browser viewport re-grounds and re-clamps the chicken.
+- Both the Terracotta and Carbon themes keep the pixel-art palette legible.
+- `npm run build` passes with no new errors.

docs/mbse/components.md

@@ -31,6 +31,7 @@ the relevant section here.
 | [6. PostgreSQL/TimescaleDB](#6-postgresqltimescaledb) | `migrations/`, `seeds/` | ✅ live — the System's own source of truth |
 | [7. Dormant components](#7-dormant-components) | `internal/actuator`, `internal/learning` | 🔴 compiled, never started |
 | [8. Auxiliary components](#8-auxiliary-components) | `cmd/webhook`, `cmd/desktop` | ✅ live — deploy + packaging, not decision logic |
+| [9. web control room — App architecture](#9-web-control-room--app-architecture) | `web/src/lib/apps.ts`, `web/src/lib/stores/windows.ts`, `web/src/lib/stores/docked.ts`, `web/src/lib/components/desktop-shell/` | ✅ live — the OS + Apps shell contract |
 
 ---
 
@@ -364,7 +365,11 @@ cross-origin (the Wails desktop webview, §8).
 Standalone deploy, versioned and released independently of the `oikos`
 binary — see [README.md §4.5](README.md#45-build--release-artifacts) for
 why "deployed" means two different release cadences depending on whether
-you mean the container or the desktop app.
+you mean the container or the desktop app. The shell-level architecture
+(window manager, app registry, docked layer) is documented separately as
+[§9 below](#9-web-control-room--app-architecture); this section covers
+the page-level concerns, §9 covers the OS + Apps contract the pages hang
+off.
 
 ---
 
@@ -496,6 +501,177 @@ functional sense.
 
 ---
 
+## 9. web control room — App architecture
+
+**Stakeholders:** anyone adding a page, adding a desktop overlay, or
+planning dynamic/third-party app installation. **Why this View earns its
+place:** §5 documents the *pages*; this View documents the *shell* they
+hang off — and the shell is the part whose contract a new app has to
+satisfy. It is also the layer where the "Oikos-as-OS" metaphor
+(desktop, icons, floating windows, a tamagotchi-style resident
+creature) is actually implemented, so the boundary between "Base OS" and
+"App" has to be explicit here or it doesn't exist anywhere.
+
+### App architecture — Internal structure
+
+| File | Role |
+|---|---|
+| `web/src/lib/apps.ts` | The App registry. Two layers: `builtinApps` (static, always installed) + `installedAppIds` (persisted, from the App Store). The public `apps` store is derived (built-in + installed); `appById` is a derived Map. `installApp`/`uninstallApp` mutate the installed set. Window-id helpers (`appWindowId`, `appIdFromWindowId`) unchanged. |
+| `web/src/app-store/catalog.ts` | The installable-app catalog: `AppManifest` (persistable metadata) + `CatalogEntry` (manifest + Lucide icon + dynamic-import loader). Static in Phase 3 (apps ship with the build); Phase 4 swaps this for a fetched `/api/v1/apps` endpoint. Declares `AppPermission` (enforcement is Phase 4). |
+| `web/src/app-store/apps/Notes.svelte` | Demo installable app — a localStorage-backed scratchpad proving the install→icon→window→uninstall lifecycle end-to-end. |
+| `web/src/lib/stores/windows.ts` | The wmkit window manager singleton + the `openAppWindow` / `openEntityWindow` / `openTaskWindow` primitives. `openAppWindow` branches on `docked` (toggles visibility) vs windowed (`wm.open`); resolves the app via `get(appById)`. |
+| `web/src/lib/stores/docked.ts` | Persisted visibility for docked apps. Absent key = visible (default-on); store holds only overrides. Deliberately does **not** import `APPS` — doing so would create a static cycle (`apps.ts` → pages → `windows.ts` → here → `apps.ts`) and fire a TDZ on `APPS` at init. |
+| `web/src/lib/stores/icons.ts` | Desktop icon grid: column/row positions, drag-to-reorder, localStorage persistence. Reactive to the `apps` store — a newly-installed app gets a free cell on the next emission; `resetIconLayout` re-seeds from the live registry, not a static snapshot. |
+| `web/src/lib/components/LazyApp.svelte` | Renders an app's lazily-loaded component (`AppDef.component` is a dynamic-import loader, not the component). Shows the shared spinner while the chunk fetches; used by both WindowLayer and DockedLayer so the loading state is uniform across app kinds. Vite's module cache makes repeat opens resolve from cache. |
+| `web/src/lib/components/desktop-shell/Desktop.svelte` | Full-viewport surface: background, icons, task launcher, `<WindowLayer />`, `<DockedLayer />`, taskbar. Reads `$apps` (the derived store) so installs reflect immediately. |
+| `web/src/lib/components/desktop-shell/WindowLayer.svelte` | Floating-window stack (z-40). Resolves window id → content component; renders shared titlebar chrome. The orphan-close `$effect` is reactive on `$appById` — reinstalling an app revives its persisted window, uninstalling closes it. |
+| `web/src/lib/components/desktop-shell/DockedLayer.svelte` | Docked-app overlay (z-45). Renders `$apps.filter(a => a.docked)` gated on `dockedVisibility`. Replaces the previously-hardcoded `<MascotLayer />`. |
+| `web/src/lib/components/desktop-shell/Taskbar.svelte` | Window buttons + tray. Renders from `wmState.order`; resolves icons via `$appById`. |
+| `web/src/pages/AppStore.svelte` | The App Store — lists the catalog, shows install state, install/uninstall. Installing makes the app appear on the desktop immediately (no reload) via the reactive `apps` store; uninstalling closes any open window for that app via WindowLayer's orphan-close effect. |
+
+### App architecture — The App contract
+
+```typescript
+interface AppDef {
+  id: string                 // unique; window IDs are "app:<id>"
+  title: string              // desktop icon label + window titlebar
+  icon: Component            // Lucide icon (desktop icon + taskbar)
+  component: () => Promise<{ default: Component }>  // dynamic-import loader
+  docked?: boolean           // true = Docked Layer app, no window
+  noIcon?: boolean           // true = registered but no desktop icon
+  width?: number; height?: number; minWidth?: number; minHeight?: number
+                             // required for windowed, forbidden for docked
+  badge?: (s: DashboardSummary | null) => number
+}
+```
+
+`component` is a dynamic-import loader (`() => import('../pages/X.svelte')`),
+not the component itself. Desktop icons render from metadata alone (id,
+title, icon — all static), the component chunk fetches on first window
+open, and Vite code-splits each app into its own chunk (Phase 2). The
+mascot uses the same path — `() => import('./mascot/MascotLayer.svelte')`
+— which also defers the mascot's module graph until after `apps.ts` has
+finished initializing, breaking what would otherwise be a static cycle
+(`apps.ts` → `MascotLayer` → `Mascot.svelte` → `icons.ts` → `apps.ts`).
+
+Two app kinds, picked by one flag:
+
+| Kind | Window | Titlebar | Taskbar | Opened by |
+|---|---|---|---|---|
+| **Windowed** (default) | wmkit floating window | yes | yes | `openAppWindow` → `wm.open` |
+| **Docked** (`docked: true`) | none — renders on the Docked Layer | no | no | `openAppWindow` → `toggleDocked` |
+
+Apps receive **no props** from the shell. They import the OS-service
+surface (below) directly. The shell→app edge is one-way.
+
+### App architecture — The OS-service surface (AppOS)
+
+The stable set of `$lib` exports an App may import. Everything else in
+`$lib` is shell-internal and may change without notice. This is a
+**documentation contract** today (apps are compiled in); it becomes an
+**enforced sandbox boundary** the moment third-party app installation
+(Phase 3 in [the plan](../../plans/2026-07-21-frontend-os-apps-architecture.md)) lands.
+
+| Service | Import |
+|---|---|
+| Open an app window | `openAppWindow(id)` from `$lib/stores/windows` |
+| Open an entity window | `openEntityWindow(slug)` from `$lib/stores/windows` |
+| Open a task window | `openTaskWindow(sessionId, title)` from `$lib/stores/windows` |
+| Dashboard summary | `summary`, `subscribeContext` from `$lib/stores/context` |
+| Live events | `subscribeEvents` from `$lib/stores/events` |
+| Per-session chat / workspace / activity | `chatFor`, `workspaceFor`, `activityLogFor` from `$lib/stores/{chat,workspace,activity}` |
+| REST API | `$lib/api` (generated from OpenAPI, [ADR-0004](../adr/0004-openapi-first.md)) |
+| UI primitives | `$lib/components/ui/*` |
+| Theme | `getTheme`, `setTheme` from `$lib/stores/theme.svelte` |
+
+### App architecture — Content resolution
+
+Window ids are namespaced so the window layer resolves content purely
+from the id, with no extra bookkeeping — which is also why persisted
+windows hydrate correctly across reloads:
+
+| Id shape | Renders |
+|---|---|
+| `app:<id>` | the registry app's component (`appById.get(id).component`) |
+| `session:<id>` | `SessionChatWindow` (per-session chat) |
+| `new-task` | `NewTaskChat` (singleton compose) |
+| bare slug (`type:identifier`) | `EntityDetailContent` (fallback) |
+
+A hydrated `app:<id>` window whose id no longer matches a registry entry
+(an app removed since the layout was persisted) self-closes — the
+orphan-close `$effect` in `WindowLayer.svelte` sweeps it on mount.
+
+### App architecture — Current population
+
+Seven windowed apps + one docked app:
+
+| App | Kind | Badge |
+|---|---|---|
+| `tasks` | windowed | — |
+| `kb` | windowed | — |
+| `ops` | windowed | `approvals_pending` |
+| `signals` | windowed | open signal count |
+| `knowledge` | windowed | — |
+| `learning` | windowed | — |
+| `settings` | windowed | — |
+| `mascot` (Cluck) | **docked** | — |
+
+The mascot is the first docked app and the reason the docked kind
+exists; before this View it was a hardcoded `<MascotLayer />` in
+`Desktop.svelte`, not a registry entry. Its persistent model
+(`web/src/lib/mascot/state.svelte.ts`, localStorage) and sprite cache
+(`sprites.ts`) are module-scoped, so toggling visibility (unmount) and
+restoring (remount) loses no state — this is why `docked` visibility is
+a plain `{#if}` gate rather than a `keepAlive` mechanism.
+
+### App architecture — Designed extension points (documented, not built)
+
+| Extension | Mechanism when built | Trigger |
+|---|---|---|
+| Titlebar actions | `titlebarActions?: Component` on `AppDef`, rendered left of min/max/close | First app that needs one |
+| App-scoped state | `state?: () => Record<string, unknown>` on `AppDef` | First app with cross-mount state that isn't module-scoped |
+| `onRegister` handshake | called with a scoped AppOS capability object | Phase 3 (dynamic install) |
+| Third-party manifests | `AppManifest` JSON + `/api/v1/apps` + permission model | Phase 3 |
+
+Documenting these now prevents the current contract from painting itself
+into a corner; building them now would be speculative. (Lazy-loaded
+components were on this list and shipped in Phase 2 — `component` is now
+`() => Promise<{ default: Component }>` and Vite code-splits each app.)
+
+### App architecture — Status and known issues
+
+Phase 1 (the docked kind, mascot-as-app, the docked visibility store) and
+Phase 2 (lazy component loading — `component` as dynamic-import loader,
+`LazyApp.svelte` for uniform loading state, per-app code-splitting) have
+landed. Open items, by phase:
+
+- **Phase 3 (dynamic install):** the AppOS table above becomes a real
+  injected capability object, not a documentation table; permissions
+  enforced at the store-access boundary; `AppManifest` format +
+  `/api/v1/apps` endpoint + install flow.
+- **Late-registering apps (Phase 3 prerequisite):** `icons.ts:48` builds
+  `appIds` once at module load to validate persisted positions — fine
+  today (all apps are in the static `APPS` array; only their components
+  are lazy), fragile the moment apps register post-load. When dynamic
+  registration lands, revalidate against the live registry, not the
+  import-time snapshot. Likewise `WindowLayer`'s orphan-close `$effect`
+  must be gated on registry-ready so a not-yet-loaded app's persisted
+  window isn't killed on hydration.
+
+The static-cycle trap that bit this View during Phase 1 implementation is
+now resolved by Phase 2's lazy loading — recording it for context:
+
+- `apps.ts` no longer statically imports any page or the mascot (they're
+  all `() => import(...)`), so there's no static edge from `apps.ts` into
+  the mascot/page module graph to cycle through `icons.ts` back to `APPS`.
+  The earlier `LazyMascot.svelte` wrapper (Phase 1's cycle break) was
+  deleted in Phase 2 — the lazy loader in the registry replaces it.
+  `docked.ts` still must not import `APPS` (it's reached from `apps.ts`'s
+  graph via `windows.ts`), and doesn't — defaults are implicit
+  (absent key = visible).
+
+---
+
 ## Keeping this document current
 
 The same discipline as README.md's closing note applies here, scoped to

docs/operations/README.md

@@ -0,0 +1,18 @@
+# Operations runbooks
+
+Step-by-step procedures for operating the homelab. These complement the
+agent-facing skill files in [`.agents/skills/`](../../.agents/skills/) (which
+are machine-actionable) and the deploy scripts in
+[`scripts/`](../../scripts/) (which are executable).
+
+| Runbook | Scope |
+| ------- | ----- |
+| [rollback.md](rollback.md) | Rollback a deploy: checkout SHA + pg_restore |
+
+For the deploy pipeline itself see
+[`scripts/deploy.sh`](../../scripts/deploy.sh), the watchdog at
+[`scripts/watchdog.sh`](../../scripts/watchdog.sh), and the cutover checklist
+at [`scripts/cutover-checklist.md`](../../scripts/cutover-checklist.md). The
+risk classification for any mutation is defined in
+[`seeds/policy.yaml`](../../seeds/policy.yaml) — run `oikos` MCP `preflight`
+to check the class before acting.

internal/actuator/circuit_breaker_test.go

@@ -0,0 +1,109 @@
+package actuator
+
+import (
+	"testing"
+	"time"
+)
+
+func TestNewCircuitBreakerDefaults(t *testing.T) {
+	cb := newCircuitBreaker(0, 0)
+	if cb.threshold != 3 {
+		t.Errorf("threshold = %d, want 3", cb.threshold)
+	}
+	if cb.cooldownS != 300 {
+		t.Errorf("cooldownS = %d, want 300", cb.cooldownS)
+	}
+
+	cb = newCircuitBreaker(5, 60)
+	if cb.threshold != 5 {
+		t.Errorf("threshold = %d, want 5", cb.threshold)
+	}
+	if cb.cooldownS != 60 {
+		t.Errorf("cooldownS = %d, want 60", cb.cooldownS)
+	}
+}
+
+func TestCircuitBreakerIsOpenFresh(t *testing.T) {
+	cb := newCircuitBreaker(3, 60)
+	if cb.isOpen("host:A") {
+		t.Errorf("fresh circuit should be closed, got open")
+	}
+}
+
+func TestCircuitBreakerOpensAtThreshold(t *testing.T) {
+	cb := newCircuitBreaker(3, 60)
+	// threshold-1 failures → still closed
+	cb.recordFailure("host:A")
+	cb.recordFailure("host:A")
+	if cb.isOpen("host:A") {
+		t.Fatalf("circuit should be closed after threshold-1 failures")
+	}
+	// one more → open
+	cb.recordFailure("host:A")
+	if !cb.isOpen("host:A") {
+		t.Fatalf("circuit should be open after threshold failures")
+	}
+}
+
+func TestCircuitBreakerClosesAfterCooldown(t *testing.T) {
+	cb := newCircuitBreaker(1, 60)
+	// Force open
+	cb.recordFailure("host:A")
+	if !cb.isOpen("host:A") {
+		t.Fatalf("circuit should be open")
+	}
+	// Manipulate the cooldown timestamp to the past to simulate expiry.
+	cb.mu.Lock()
+	cb.cooldowns["host:A"] = time.Now().Add(-1 * time.Second)
+	cb.mu.Unlock()
+
+	if cb.isOpen("host:A") {
+		t.Fatalf("circuit should be closed after cooldown expired")
+	}
+	// Failure count should have been reset by isOpen.
+	cb.mu.Lock()
+	got := cb.failures["host:A"]
+	cb.mu.Unlock()
+	if got != 0 {
+		t.Errorf("failure count after cooldown reset = %d, want 0", got)
+	}
+}
+
+func TestCircuitBreakerRecordSuccessResets(t *testing.T) {
+	cb := newCircuitBreaker(3, 60)
+	cb.recordFailure("host:A")
+	cb.recordFailure("host:A")
+
+	cb.recordSuccess("host:A")
+
+	cb.mu.Lock()
+	got := cb.failures["host:A"]
+	cb.mu.Unlock()
+	if got != 0 {
+		t.Errorf("failure count after success = %d, want 0", got)
+	}
+	if cb.isOpen("host:A") {
+		t.Errorf("circuit should be closed after success reset")
+	}
+}
+
+func TestCircuitBreakerPerTargetIsolation(t *testing.T) {
+	cb := newCircuitBreaker(2, 60)
+	cb.recordFailure("host:A")
+	cb.recordFailure("host:A") // host:A now at threshold → open
+
+	if !cb.isOpen("host:A") {
+		t.Fatalf("host:A should be open")
+	}
+	if cb.isOpen("host:B") {
+		t.Errorf("host:B should be closed (isolated from host:A)")
+	}
+
+	// host:B has no failures recorded
+	cb.mu.Lock()
+	gotB := cb.failures["host:B"]
+	cb.mu.Unlock()
+	if gotB != 0 {
+		t.Errorf("host:B failure count = %d, want 0", gotB)
+	}
+}

internal/actuator/ssh_test.go

@@ -0,0 +1,151 @@
+package actuator
+
+import (
+	"context"
+	"errors"
+	"net"
+	"testing"
+	"time"
+
+	"golang.org/x/crypto/ssh"
+)
+
+func TestSSHErrorClassString(t *testing.T) {
+	cases := []struct {
+		class SSHErrorClass
+		want  string
+	}{
+		{SSHErrorNetwork, "network"},
+		{SSHErrorAuth, "auth"},
+		{SSHErrorTimeout, "timed_out"},
+		{SSHErrorRemote, "remote"},
+		{SSHErrorOther, "other"},
+		{SSHErrorClass(999), "unknown"},
+	}
+	for _, c := range cases {
+		if got := c.class.String(); got != c.want {
+			t.Errorf("SSHErrorClass(%d).String() = %q, want %q", c.class, got, c.want)
+		}
+	}
+}
+
+// timeoutNetErr is a custom net.Error implementation for testing.
+type timeoutNetErr struct {
+	timeout bool
+	msg     string
+}
+
+func (e *timeoutNetErr) Error() string   { return e.msg }
+func (e *timeoutNetErr) Timeout() bool   { return e.timeout }
+func (e *timeoutNetErr) Temporary() bool { return false }
+
+func TestClassifySSHError(t *testing.T) {
+	// ssh.ExitError fields are unexported, but classifySSHError only checks
+	// for the type via errors.As, so the zero value is sufficient.
+	exitErr := &ssh.ExitError{}
+
+	cases := []struct {
+		name string
+		err  error
+		want SSHErrorClass
+	}{
+		{"nil", nil, SSHErrorOther},
+		{"deadline exceeded", context.DeadlineExceeded, SSHErrorTimeout},
+		{"net error timeout true", &timeoutNetErr{timeout: true, msg: "i/o timeout"}, SSHErrorNetwork},
+		{"net error timeout false", &timeoutNetErr{timeout: false, msg: "connection refused"}, SSHErrorNetwork},
+		{"unable to authenticate", errors.New("unable to authenticate, no supported methods remain"), SSHErrorAuth},
+		{"no supported methods remain", errors.New("no supported methods remain (server sent publickey)"), SSHErrorAuth},
+		{"ssh handshake failed", errors.New("ssh: handshake failed: read tcp -> eof"), SSHErrorAuth},
+		{"publickey", errors.New("publickey denied"), SSHErrorAuth},
+		{"permission denied", errors.New("permission denied (publickey)"), SSHErrorAuth},
+		{"exit error", exitErr, SSHErrorRemote},
+		{"generic error", errors.New("something went wrong"), SSHErrorOther},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			if got := classifySSHError(c.err); got != c.want {
+				t.Errorf("classifySSHError(%v) = %v, want %v", c.err, got, c.want)
+			}
+		})
+	}
+}
+
+func TestParseProcedure(t *testing.T) {
+	cases := []struct {
+		name    string
+		data    []byte
+		wantErr bool
+		wantLen int
+	}{
+		{
+			name:    "valid with steps",
+			data:    []byte(`{"steps":[{"runner":"shell","command":"echo hi"}]}`),
+			wantErr: false,
+			wantLen: 1,
+		},
+		{
+			name:    "invalid json",
+			data:    []byte(`{not json`),
+			wantErr: true,
+		},
+		{
+			name:    "empty bytes",
+			data:    []byte{},
+			wantErr: true,
+		},
+		{
+			name:    "valid no steps key",
+			data:    []byte(`{"foo":"bar"}`),
+			wantErr: false,
+			wantLen: 0,
+		},
+		{
+			name:    "valid with extra fields",
+			data:    []byte(`{"extra":"ignored","steps":[{"runner":"verify","command":"true"}],"more":123}`),
+			wantErr: false,
+			wantLen: 1,
+		},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			proc, err := ParseProcedure(c.data)
+			if c.wantErr {
+				if err == nil {
+					t.Fatalf("expected error, got nil (proc=%+v)", proc)
+				}
+				return
+			}
+			if err != nil {
+				t.Fatalf("unexpected error: %v", err)
+			}
+			if len(proc.Steps) != c.wantLen {
+				t.Errorf("got %d steps, want %d", len(proc.Steps), c.wantLen)
+			}
+		})
+	}
+}
+
+func TestSetDefaultSSHTimeout(t *testing.T) {
+	mu.Lock()
+	orig := defaultSSHTimeout
+	mu.Unlock()
+	defer func() {
+		mu.Lock()
+		defaultSSHTimeout = orig
+		mu.Unlock()
+	}()
+
+	newTimeout := 42 * time.Second
+	SetDefaultSSHTimeout(newTimeout)
+
+	mu.Lock()
+	got := defaultSSHTimeout
+	mu.Unlock()
+
+	if got != newTimeout {
+		t.Errorf("defaultSSHTimeout = %v, want %v", got, newTimeout)
+	}
+}
+
+// Ensure timeoutNetErr satisfies net.Error at compile time.
+var _ net.Error = (*timeoutNetErr)(nil)

internal/audit/audit.go

@@ -0,0 +1,133 @@
+// Package audit produces read-only drift reports over the knowledge graph and
+// monitoring state. It is the shared engine behind the
+// /api/v1/audit/drift endpoint and the audit_knowledge_graph MCP tool.
+//
+// It surfaces the structural gaps an operator otherwise discovers only by
+// accident: orphan check entities, checks targeting retired entities, probes
+// stuck down/unknown, unmonitored declared types, and live edges pointing at
+// destroyed/deprecated targets. Live-infra discovery (pct/docker/certs) is a
+// follow-up that needs host-hop execution; these categories are pure DB
+// queries, so the report is cheap, safe to run unattended, and testable.
+package audit
+
+import (
+	"context"
+
+	"github.com/dtoro/oikos/internal/db"
+)
+
+// Finding is one drift item the operator should look at.
+type Finding struct {
+	Category         string   `json:"category"`
+	Severity         string   `json:"severity"` // info | warning | critical
+	Count            int      `json:"count"`
+	Entities         []string `json:"entities"`
+	Evidence         string   `json:"evidence"`
+	SuggestedRunbook string   `json:"suggested_runbook"`
+}
+
+// Summary tallies findings by category.
+type Summary struct {
+	TotalFindings int            `json:"total_findings"`
+	ByCategory    map[string]int `json:"by_category"`
+}
+
+// Report runs every drift check and returns the findings plus a summary.
+func Report(ctx context.Context, pool *db.Pool) ([]Finding, Summary) {
+	specs := []struct {
+		finding Finding
+		query   string
+	}{
+		{
+			Finding{Category: "orphan_checks", Severity: "warning",
+				Evidence:         "check entities with truncated/random slugs (legacy shortSlug bug), no live target",
+				SuggestedRunbook: "scripts/cleanup-orphan-checks.sh"},
+			`SELECT e.slug FROM entities e
+			 WHERE e.type = 'check'
+			   AND e.slug ~ '^check:(ping|ssh-script|disk):[0-9a-f]{8}$'`,
+		},
+		{
+			Finding{Category: "dead_checks", Severity: "warning",
+				Evidence:         "enabled check_defs whose target entity is deprecated/destroyed",
+				SuggestedRunbook: "lifecycle-deprecate-node / lifecycle-destroy-node"},
+			`SELECT e.slug FROM check_defs cd
+			 JOIN entities e ON e.id = cd.entity_id
+			 JOIN entities tgt ON tgt.id = cd.target_id
+			 WHERE cd.enabled AND tgt.state IN ('deprecated','destroyed')`,
+		},
+		{
+			Finding{Category: "down_checks", Severity: "critical",
+				Evidence:         "enabled checks reporting health=down",
+				SuggestedRunbook: "service-health-check"},
+			`SELECT e.slug FROM check_defs cd JOIN entities e ON e.id = cd.entity_id
+			 WHERE cd.enabled AND cd.last_health = 'down'`,
+		},
+		{
+			Finding{Category: "unknown_checks", Severity: "warning",
+				Evidence:         "enabled checks that ran but reported health=unknown (likely misconfigured probe)",
+				SuggestedRunbook: "knowledge-graph-audit"},
+			`SELECT e.slug FROM check_defs cd JOIN entities e ON e.id = cd.entity_id
+			 WHERE cd.enabled AND cd.last_health = 'unknown'`,
+		},
+		{
+			Finding{Category: "unmonitored", Severity: "warning",
+				Evidence:         "active entities whose type declares monitoring but have no enabled check_def",
+				SuggestedRunbook: "knowledge-graph-audit"},
+			`SELECT DISTINCT e.slug FROM signals sg
+			 JOIN entities e ON e.id = sg.target_entity_id
+			 WHERE sg.kind = 'unmonitored' AND sg.state IN ('raised','acknowledged','acting')`,
+		},
+		{
+			Finding{Category: "dangling_edges", Severity: "warning",
+				Evidence:         "live relationships (hosts/provides/mounts) pointing at destroyed/deprecated targets",
+				SuggestedRunbook: "lifecycle-destroy-node"},
+			`SELECT src.slug || ' -' || r.type || '-> ' || tgt.slug FROM relationships r
+			 JOIN entities src ON src.id = r.source_id
+			 JOIN entities tgt ON tgt.id = r.target_id
+			 WHERE r.valid_to IS NULL
+			   AND src.state NOT IN ('destroyed','deprecated')
+			   AND tgt.state IN ('destroyed','deprecated')`,
+		},
+		{
+			Finding{Category: "polluted_attrs", Severity: "warning",
+				Evidence:         "routing-critical attributes carrying prose (breaks resolution) — e.g. host='hubris (confirmed via pct…')",
+				SuggestedRunbook: "knowledge-graph-audit"},
+			`SELECT slug || ': host=' || (attributes->>'host') FROM entities
+			 WHERE attributes->>'host' IS NOT NULL
+			   AND (attributes->>'host') ~ '[ (]'`,
+		},
+	}
+
+	findings := make([]Finding, 0, len(specs))
+	summary := Summary{ByCategory: map[string]int{}}
+	for _, sp := range specs {
+		f := runFinding(ctx, pool, sp.finding, sp.query)
+		findings = append(findings, f)
+		summary.TotalFindings += f.Count
+		summary.ByCategory[f.Category] = f.Count
+	}
+	return findings, summary
+}
+
+const entityCap = 50
+
+// runFinding runs a single-column slug query and folds the rows into a Finding.
+func runFinding(ctx context.Context, pool *db.Pool, f Finding, query string) Finding {
+	rows, err := pool.Query(ctx, query)
+	if err != nil {
+		f.Evidence = f.Evidence + " (query error: " + err.Error() + ")"
+		return f
+	}
+	defer rows.Close()
+	for rows.Next() {
+		var slug string
+		if err := rows.Scan(&slug); err != nil {
+			continue
+		}
+		f.Count++
+		if len(f.Entities) < entityCap {
+			f.Entities = append(f.Entities, slug)
+		}
+	}
+	return f
+}

internal/audit/audit_test.go

@@ -0,0 +1,69 @@
+package audit
+
+import (
+	"context"
+	"testing"
+
+	"github.com/dtoro/oikos/internal/db"
+	"github.com/google/uuid"
+)
+
+// Integration tests against a real Postgres, guarded by
+// OIKOS_TEST_DATABASE_URL (same convention as internal/scheduler).
+
+func newAuditPool(t *testing.T) *db.Pool {
+	t.Helper()
+	base := getenvOrDefault("OIKOS_TEST_DATABASE_URL", "")
+	if base == "" {
+		t.Skip("OIKOS_TEST_DATABASE_URL not set — skipping integration test")
+	}
+	return createTestDB(t, base)
+}
+
+func TestReportFlagsOrphanAndDeadAndDown(t *testing.T) {
+	pool := newAuditPool(t)
+	ctx := context.Background()
+
+	// An orphan check entity (truncated random slug, the legacy bug shape).
+	mustExec(t, pool, ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		VALUES ($1,'check:ssh-script:0d31fdd1','check','check:ssh-script:0d31fdd1','active','{}'::jsonb,1,now(),now())`, uuid.New())
+
+	// An active entity + a check_def on it stuck down.
+	target := uuid.New()
+	mustExec(t, pool, ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		VALUES ($1,'service:demo','service','demo','active','{}'::jsonb,1,now(),now())`, target)
+	checkE := uuid.New()
+	mustExec(t, pool, ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		VALUES ($1,'check:http:service:demo:0','check','c','active','{}'::jsonb,1,now(),now())`, checkE)
+	mustExec(t, pool, ctx, `INSERT INTO check_defs (entity_id, target_id, target_type, kind, config, interval_s, timeout_s, enabled, last_run_at, last_health)
+		VALUES ($1,$2,'service','http','{}'::jsonb,60,30,true,now(),'down')`, checkE, target)
+
+	// A deprecated entity still carrying an enabled check (dead_checks).
+	dep := uuid.New()
+	mustExec(t, pool, ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		VALUES ($1,'service:old','service','old','deprecated','{}'::jsonb,1,now(),now())`, dep)
+	depCheck := uuid.New()
+	mustExec(t, pool, ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		VALUES ($1,'check:http:service:old:0','check','c','active','{}'::jsonb,1,now(),now())`, depCheck)
+	mustExec(t, pool, ctx, `INSERT INTO check_defs (entity_id, target_id, target_type, kind, config, interval_s, timeout_s, enabled, last_run_at)
+		VALUES ($1,$2,'service','http','{}'::jsonb,60,30,true,now())`, depCheck, dep)
+
+	findings, summary := Report(ctx, pool)
+
+	byCat := map[string]int{}
+	for _, f := range findings {
+		byCat[f.Category] = f.Count
+	}
+	if byCat["orphan_checks"] < 1 {
+		t.Errorf("orphan_checks = %d, want >=1", byCat["orphan_checks"])
+	}
+	if byCat["down_checks"] < 1 {
+		t.Errorf("down_checks = %d, want >=1", byCat["down_checks"])
+	}
+	if byCat["dead_checks"] < 1 {
+		t.Errorf("dead_checks = %d, want >=1", byCat["dead_checks"])
+	}
+	if summary.TotalFindings < 3 {
+		t.Errorf("TotalFindings = %d, want >=3", summary.TotalFindings)
+	}
+}

internal/audit/testutil_test.go

@@ -0,0 +1,67 @@
+package audit
+
+import (
+	"context"
+	"fmt"
+	"math/rand"
+	"os"
+	"strings"
+	"testing"
+
+	"github.com/dtoro/oikos/internal/db"
+	"github.com/jackc/pgx/v5"
+)
+
+// createTestDB provisions a throwaway migrated database, same convention as
+// internal/scheduler/coverage_test.go.
+func createTestDB(t *testing.T, baseURL string) *db.Pool {
+	t.Helper()
+	ctx := context.Background()
+
+	admin, err := pgx.Connect(ctx, baseURL)
+	if err != nil {
+		t.Fatalf("connect admin: %v", err)
+	}
+	dbName := fmt.Sprintf("oikos_aud_%08x", rand.Int63())
+	if _, err := admin.Exec(ctx, "CREATE DATABASE "+dbName); err != nil {
+		admin.Close(ctx)
+		t.Fatalf("create test db: %v", err)
+	}
+	admin.Close(ctx)
+
+	at := strings.LastIndex(baseURL, "/")
+	testURL := baseURL[:at+1] + dbName
+	if q := strings.Index(baseURL[at:], "?"); q >= 0 {
+		testURL += baseURL[at+q:]
+	}
+
+	pool, err := db.New(ctx, testURL)
+	if err != nil {
+		t.Fatalf("connect test db: %v", err)
+	}
+	if err := pool.Migrate(ctx); err != nil {
+		t.Fatalf("migrate: %v", err)
+	}
+	t.Cleanup(func() {
+		pool.Close()
+		if admin, err := pgx.Connect(ctx, baseURL); err == nil {
+			admin.Exec(ctx, "DROP DATABASE IF EXISTS "+dbName+" WITH (FORCE)")
+			admin.Close(ctx)
+		}
+	})
+	return pool
+}
+
+func getenvOrDefault(key, def string) string {
+	if v := os.Getenv(key); v != "" {
+		return v
+	}
+	return def
+}
+
+func mustExec(t *testing.T, pool *db.Pool, ctx context.Context, q string, args ...any) {
+	t.Helper()
+	if _, err := pool.Exec(ctx, q, args...); err != nil {
+		t.Fatalf("exec %s: %v", q, err)
+	}
+}

internal/checkdefaults/defaults.go

@@ -1,38 +1,540 @@
+// Package checkdefaults derives an entity's default check_defs from the
+// monitoring kinds its type declares in seeds/ontology.yaml.
+//
+// The type says WHAT to watch (`service: [http, process]`); this package
+// works out HOW — which concrete check_defs rows to write, and what host,
+// script or URL each needs. Deriving config here rather than in YAML keeps
+// the ontology declarative and keeps address resolution (which has to walk
+// the graph) in code.
 package checkdefaults
 
 import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"log/slog"
+	"strings"
 
+	"github.com/dtoro/oikos/internal/ontology"
 	"github.com/google/uuid"
 	"github.com/jackc/pgx/v5"
 )
 
-type CheckDef struct {
-	Kind       string
-	Script     string
-	Host       string
-	User       string
-	Port       int
-	Thresholds map[string]any
-	Extra      map[string]any
+// Semantic monitoring kinds, as declared on entity types. These are not
+// check_defs.kind values — one semantic kind can expand to several concrete
+// checks (`resource` becomes four ssh-script rows).
+const (
+	KindPing       = "ping"
+	KindResource   = "resource"
+	KindUpdates    = "updates"
+	KindProcess    = "process"
+	KindHTTP       = "http"
+	KindCapacity   = "capacity"
+	KindBackup     = "backup-freshness"
+	KindCertExpiry = "cert-expiry"
+	KindVMStatus   = "vm-status"
+	KindDNS        = "dns"
+)
+
+// defaultBackupMaxAge is how long a backup target may go without a new
+// artifact before it is stale. A day suits the nightly jobs in this lab;
+// override per target with `backup_max_age_s` in the entity's attributes.
+const defaultBackupMaxAge = 86400
+
+// Target is the entity default checks are being ensured for.
+type Target struct {
+	ID   uuid.UUID
+	Slug string
+	Type string
+	// Name is the entity's name column, not an attribute. The old code read
+	// attrs["name"], which is never populated — seeds put `name` beside
+	// `attributes`, not inside it — so every service silently produced no
+	// process check.
+	Name  string
+	Attrs []byte
 }
 
-func ResolveHost(attrs map[string]any) string {
+// Result reports what Ensure did, so callers can log a type that declared
+// monitoring but produced nothing instead of failing silently.
+type Result struct {
+	Created int
+	// Skipped records kinds that were declared but could not be built, with
+	// the reason. A non-empty Skipped on an active entity is a real gap.
+	Skipped []Skip
+	// Undeclared is true when no ancestor of the type declared monitoring —
+	// an ontology gap rather than a fleet gap.
+	Undeclared bool
+}
+
+// Skip is one declared-but-unbuilt check kind.
+type Skip struct {
+	Kind   string
+	Reason string
+}
+
+type checkDef struct {
+	kind     string
+	config   map[string]any
+	interval int32
+}
+
+// Ensure writes the default check_defs for one entity, idempotently.
+//
+// Returns the number of checks created. An entity whose type declares
+// monitoring it cannot satisfy comes back with a populated Skipped rather
+// than an error — a missing address is a modelling gap, not a failure of
+// this call.
+func Ensure(ctx context.Context, tx pgx.Tx, tree *ontology.TypeTree, t Target) (Result, error) {
+	var res Result
+
+	if _, err := tx.Exec(ctx,
+		`INSERT INTO entity_status (entity_id, health, updated_at)
+		 VALUES ($1, 'unknown', now())
+		 ON CONFLICT (entity_id) DO NOTHING`, t.ID); err != nil {
+		return res, fmt.Errorf("entity_status %s: %w", t.Slug, err)
+	}
+
+	mon := tree.Monitoring(t.Type)
+	if !mon.Declared {
+		res.Undeclared = true
+		return res, nil
+	}
+	if mon.None() {
+		return res, nil
+	}
+
+	var attrs map[string]any
+	if len(t.Attrs) > 0 {
+		_ = json.Unmarshal(t.Attrs, &attrs)
+	}
+	if attrs == nil {
+		attrs = map[string]any{}
+	}
+
+	// Per-entity override: an explicit `monitoring` attribute wins over the
+	// type declaration. A single entity can opt out (monitoring: none) or pick
+	// different kinds without introducing a new type — e.g. service:haos opts
+	// out because its VM is already covered by a vm-status check and the
+	// service can't be SSH-probed (haos blocks SSH).
+	if mo, ok := attrs["monitoring"]; ok {
+		mon = resolveMonitoringAttr(mo, mon)
+		if mon.None() {
+			return res, nil
+		}
+	}
+
+	// A service has no address of its own — it lives on the container that
+	// provides it. Fall back to the graph before giving up.
+	host := resolveHost(attrs)
+	if host == "" {
+		hostAttrs, err := hostViaGraph(ctx, tx, t.ID)
+		if err != nil {
+			return res, fmt.Errorf("resolve host for %s: %w", t.Slug, err)
+		}
+		host = resolveHost(hostAttrs)
+		if user := resolveSSHUser(hostAttrs); host != "" && user != "root" {
+			attrs["ssh"] = hostAttrs["ssh"]
+		}
+	}
+	user := resolveSSHUser(attrs)
+	port := resolveSSHPort(attrs)
+
+	var defs []checkDef
+	for _, kind := range mon.Kinds {
+		built, reason := buildKind(kind, t, attrs, host, user, port)
+		if len(built) == 0 {
+			res.Skipped = append(res.Skipped, Skip{Kind: kind, Reason: reason})
+			continue
+		}
+		defs = append(defs, built...)
+	}
+
+	for i, def := range defs {
+		created, err := writeCheck(ctx, tx, t, i, def)
+		if err != nil {
+			return res, fmt.Errorf("check %s/%s: %w", t.Slug, def.kind, err)
+		}
+		if created {
+			res.Created++
+		}
+	}
+	return res, nil
+}
+
+// resolveMonitoringAttr turns an entity's `monitoring` attribute into a
+// MonitoringResolution that overrides the type's declaration. Accepts the
+// scalar "none" (or empty) to opt out, or a list of kind strings to override.
+func resolveMonitoringAttr(v any, fallback ontology.MonitoringResolution) ontology.MonitoringResolution {
+	switch vv := v.(type) {
+	case string:
+		if vv == "none" || vv == "" {
+			return ontology.MonitoringResolution{Declared: true, Source: "attribute"}
+		}
+	case []any:
+		kinds := make([]string, 0, len(vv))
+		for _, k := range vv {
+			if s, ok := k.(string); ok && s != "" {
+				kinds = append(kinds, s)
+			}
+		}
+		return ontology.MonitoringResolution{Declared: true, Kinds: kinds, Source: "attribute"}
+	}
+	return fallback
+}
+
+// buildKind turns one declared semantic kind into concrete check_defs, or
+// returns the reason it could not.
+func buildKind(kind string, t Target, attrs map[string]any, host, user string, port int) ([]checkDef, string) {
+	ssh := func(script string, args ...string) checkDef {
+		cfg := map[string]any{"script": script, "host": host}
+		if user != "" && user != "root" {
+			cfg["user"] = user
+		}
+		if port != 0 && port != 22 {
+			cfg["port"] = port
+		}
+		if len(args) > 0 && args[0] != "" {
+			cfg["args"] = args[0]
+		}
+		return checkDef{kind: "ssh-script", config: cfg, interval: 60}
+	}
+
+	switch kind {
+	case KindPing:
+		if host == "" {
+			return nil, "no address on the entity or its host"
+		}
+		return []checkDef{{kind: "ping", config: map[string]any{"host": host}, interval: 30}}, ""
+
+	case KindResource:
+		if host == "" {
+			return nil, "no address on the entity or its host"
+		}
+		return []checkDef{
+			ssh("cpu_check.sh"), ssh("memory_check.sh"),
+			ssh("load_check.sh"), ssh("disk_usage_check.sh"),
+		}, ""
+
+	case KindUpdates:
+		if host == "" {
+			return nil, "no address on the entity or its host"
+		}
+		// Daily. updates_check.sh runs `apt update` against the distro
+		// mirrors; the shared 60s ssh-script default would have meant 1,440
+		// mirror hits per machine per day to answer a question whose answer
+		// changes about once a day.
+		u := ssh("updates_check.sh")
+		u.interval = 86400
+		return []checkDef{u}, ""
+
+	case KindCapacity:
+		if host == "" {
+			return nil, "no address on the entity or its host"
+		}
+		return []checkDef{ssh("disk_usage_check.sh")}, ""
+
+	case KindProcess:
+		if host == "" {
+			return nil, "no address on the entity or its host"
+		}
+		// A service's name is a logical label, not usually its systemd unit
+		// or container name (matrix = matrix-synapse.service + containers).
+		// Prefer an explicit probe target when declared; process_check.sh also
+		// matches a unit prefix or a docker container as a fallback.
+		unit := ""
+		for _, key := range []string{"probe_unit", "systemd_unit", "container"} {
+			if v, _ := attrs[key].(string); v != "" {
+				unit = v
+				break
+			}
+		}
+		// Ontology intent: "http when it has a url, else a process check." A
+		// url-fronted service is already liveness-probed via http (the real
+		// endpoint, through the TLS terminator); the process check is redundant
+		// and fragile (needs host access + the exact unit/container name), and
+		// under worst-of aggregation it lets a broken supplementary probe veto
+		// a working service. Emit it only for services WITHOUT a url, or when
+		// an explicit probe_unit opts into binary-level depth.
+		if unit == "" {
+			if httpURL(t, attrs) != "" {
+				return nil, "url present and no probe_unit; http check covers liveness"
+			}
+			unit = t.Name
+		}
+		if unit == "" {
+			return nil, "no name to check a process for"
+		}
+		// process_check.sh takes the unit/container name as $1 and reports
+		// "unknown" without it.
+		return []checkDef{ssh("process_check.sh", unit)}, ""
+
+	case KindBackup:
+		// A backup target is checked from the machine that writes to it, so it
+		// needs both an address (resolved via the backs-up-to edge) and the
+		// path to look at.
+		path, _ := attrs["path"].(string)
+		if path == "" {
+			return nil, "entity carries no path attribute to check for backups"
+		}
+		if host == "" {
+			return nil, "no address on the entity or whatever backs up to it"
+		}
+		maxAge := defaultBackupMaxAge
+		if v, ok := attrs["backup_max_age_s"].(float64); ok && v > 0 {
+			maxAge = int(v)
+		}
+		cfg := map[string]any{"path": path, "host": host, "max_age_s": maxAge}
+		if user != "" && user != "root" {
+			cfg["user"] = user
+		}
+		if port != 0 && port != 22 {
+			cfg["port"] = port
+		}
+		// Daily. The freshness budget itself is a day, so probing more often
+		// cannot surface anything sooner — it just costs an SSH round trip.
+		return []checkDef{{kind: "backup-freshness", config: cfg, interval: 86400}}, ""
+
+	case KindHTTP:
+		url := httpURL(t, attrs)
+		if url == "" {
+			return nil, "no url attribute, public_host, or hostname-shaped name"
+		}
+		// max_status rather than an exact expected_status: most services sit
+		// behind Authentik and answer 302/401, which is a working service.
+		return []checkDef{{
+			kind:     "http",
+			config:   map[string]any{"url": url, "max_status": 500},
+			interval: 60,
+		}}, ""
+
+	case KindDNS:
+		// Resolve the entity's name via DNS to verify the zone is reachable.
+		// Uses the entity name (zone apex) or falls back to the slug.
+		name := t.Name
+		if name == "" {
+			name = strings.TrimPrefix(t.Slug, "zone:")
+		}
+		if name == "" {
+			return nil, "no name to resolve"
+		}
+		return []checkDef{{
+			kind:     "dns",
+			config:   map[string]any{"name": name},
+			interval: 300, // 5 min — DNS changes are rare; the cost of a miss
+			               // is a stale IP, not a service outage.
+		}}, ""
+
+	case KindCertExpiry:
+		// The host whose cert to read (SNI / cert CN). Prefer an explicit
+		// `hostname` attribute, then `cn`, then a dotted name. Hourly: expiry
+		// changes once a day, but a renewal or mis-issued cert is worth
+		// noticing within the hour.
+		host := certHost(t, attrs)
+		if host == "" {
+			return nil, "no hostname / cn / dotted name to dial for the cert"
+		}
+		// `dial` is the TLS terminator's address to connect to (Caddy's lab
+		// IP), used when the hostname doesn't resolve/reach from the scheduler.
+		// Without it the probe can't reach *.hubris.network from a container
+		// with no mesh / split-horizon DNS.
+		dial, _ := attrs["dial"].(string)
+		config := map[string]any{"host": host, "warn_days": 30, "crit_days": 7}
+		if dial != "" {
+			config["dial"] = dial
+		}
+		return []checkDef{{
+			kind:     "cert-expiry",
+			config:   config,
+			interval: 3600,
+		}}, ""
+
+	case KindVMStatus:
+		// "Is the VM powered on" via `qm status` on its Proxmox host — the
+		// right reachability probe for a VM, since many block ICMP and lack a
+		// guest agent. checkVMStatus re-reads pve_id + host at runtime.
+		if _, ok := attrs["pve_id"]; !ok {
+			return nil, "no pve_id to run qm status"
+		}
+		return []checkDef{{
+			kind:     "vm-status",
+			config:   map[string]any{},
+			interval: 60,
+		}}, ""
+	}
+
+	return nil, "no builder for this kind yet"
+}
+
+// certHost works out the hostname to TLS-dial for a certificate's expiry.
+func certHost(t Target, attrs map[string]any) string {
+	for _, key := range []string{"hostname", "cn", "san"} {
+		if v, ok := attrs[key].(string); ok && v != "" {
+			return v
+		}
+	}
+	// A dotted name is a hostname (hubris.network, media.hubris.network).
+	if strings.Contains(t.Name, ".") && !strings.Contains(t.Name, " ") {
+		return t.Name
+	}
+	return ""
+}
+
+// writeCheck upserts one check_def and its backing check entity.
+//
+// The entity upsert MUST return the row's id. The previous version generated
+// a fresh uuid, inserted ON CONFLICT (slug) DO NOTHING, then wrote a
+// check_defs row referencing that uuid. On any re-seed the slug already
+// existed, the entity insert became a no-op, and the check_defs insert
+// violated its foreign key — which aborted the whole ingest transaction and
+// made every subsequent statement fail with 25P02. Because the errors were
+// discarded, the only visible symptom was an unrelated failure much later.
+func writeCheck(ctx context.Context, tx pgx.Tx, t Target, idx int, def checkDef) (bool, error) {
+	// The full target slug, not a truncation of it. shortSlug() took the last
+	// 8 characters, so all 21 ingress routes collapsed to ".network" and
+	// generated one identical check slug — they overwrote each other and 20
+	// of them ended up with no check at all. It also collided service:jellyfin
+	// with lxc:jellyfin. Entity slugs are unique; use them.
+	checkSlug := fmt.Sprintf("check:%s:%s:%d", def.kind, t.Slug, idx)
+
+	newID, err := uuid.NewV7()
+	if err != nil {
+		newID = uuid.New()
+	}
+
+	var checkID uuid.UUID
+	err = tx.QueryRow(ctx,
+		`INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
+		 VALUES ($1, $2, 'check', $2, 'active', '{}', 1, now(), now())
+		 ON CONFLICT (slug) DO UPDATE SET updated_at = now()
+		 RETURNING id`,
+		newID, checkSlug).Scan(&checkID)
+	if err != nil {
+		return false, fmt.Errorf("upsert check entity %s: %w", checkSlug, err)
+	}
+
+	configJSON, err := json.Marshal(def.config)
+	if err != nil {
+		return false, err
+	}
+
+	// Config is derived from the seed, so the seed wins on re-ingest and
+	// attribute changes propagate. `enabled` is deliberately left alone: it
+	// is operational state an operator may have toggled.
+	// last_run_at is seeded to a random point inside the interval so checks
+	// created together do not stay in lockstep. Every check the seed creates
+	// would otherwise come due in the same instant forever: ~165 probes
+	// landing at once each minute rather than spread across it. Deliberately
+	// absent from the DO UPDATE below — a re-seed must not reset the schedule
+	// and re-herd everything.
+	tag, err := tx.Exec(ctx,
+		`INSERT INTO check_defs (entity_id, target_id, target_type, kind, config, interval_s, timeout_s, enabled, last_run_at)
+		 VALUES ($1, $2, $6, $3, $4, $5, 30, true,
+		         now() - make_interval(secs => random() * $5::int))
+		 ON CONFLICT (entity_id) DO UPDATE
+		   SET target_id = EXCLUDED.target_id, target_type = EXCLUDED.target_type,
+		       kind = EXCLUDED.kind,
+		       config = EXCLUDED.config, interval_s = EXCLUDED.interval_s,
+		       updated_at = now()`,
+		checkID, t.ID, def.kind, configJSON, def.interval, t.Type)
+	if err != nil {
+		return false, fmt.Errorf("upsert check_def %s: %w", checkSlug, err)
+	}
+	return tag.RowsAffected() > 0, nil
+}
+
+// httpURL works out what to GET for an http check.
+//
+// Ingress routes carry their hostname as the entity name rather than as an
+// attribute (`name: media.hubris.network`), and most declare no attributes at
+// all — so the name is the only thing to go on. Requiring a `url` attribute
+// left all 21 of them unmonitored, which is a shame given an ingress check is
+// the most end-to-end probe available: it exercises Caddy, DNS, TLS and the
+// upstream in one request.
+func httpURL(t Target, attrs map[string]any) string {
+	if url, ok := attrs["url"].(string); ok && url != "" {
+		return url
+	}
+	if h, ok := attrs["public_host"].(string); ok && h != "" {
+		return "https://" + h
+	}
+	// A dotted name is a hostname; a service name like "jellyfin" is not.
+	if strings.Contains(t.Name, ".") && !strings.Contains(t.Name, " ") {
+		return "https://" + t.Name
+	}
+	return ""
+}
+
+// hostViaGraph returns the attributes of the entity that hosts or provides
+// this one, so a service can inherit its container's address.
+func hostViaGraph(ctx context.Context, tx pgx.Tx, entityID uuid.UUID) (map[string]any, error) {
+	rows, err := tx.Query(ctx, `
+		SELECT e.attributes
+		FROM relationships r
+		JOIN entities e ON e.id = r.source_id
+		WHERE r.target_id = $1
+		  AND r.valid_to IS NULL
+		  -- backs-up-to points from the thing being backed up TO the target,
+		  -- so walking it backwards finds the machine that writes the backups
+		  -- — which is the only place a freshness check can run.
+		  AND r.type IN ('provides', 'hosts', 'runs-on', 'backs-up-to')
+		ORDER BY CASE r.type
+		    WHEN 'provides' THEN 0 WHEN 'runs-on' THEN 1
+		    WHEN 'backs-up-to' THEN 2 ELSE 3 END`,
+		entityID)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	for rows.Next() {
+		var raw []byte
+		if err := rows.Scan(&raw); err != nil {
+			return nil, err
+		}
+		var attrs map[string]any
+		if json.Unmarshal(raw, &attrs) != nil {
+			continue
+		}
+		if resolveHost(attrs) != "" {
+			return attrs, nil
+		}
+	}
+	return nil, rows.Err()
+}
+
+func resolveHost(attrs map[string]any) string {
+	if attrs == nil {
+		return ""
+	}
 	if ip, ok := attrs["lan_ip"].(string); ok && ip != "" {
 		return ip
 	}
+	// public_ipv4 before mesh: the scheduler container has no mesh interface,
+	// so a standalone-server reachable only by mesh IP (netbird-vps) is
+	// unprobeable even though a public IPv4 is available.
+	if ip, ok := attrs["public_ipv4"].(string); ok && ip != "" {
+		return ip
+	}
 	if mesh, ok := attrs["mesh"].(map[string]any); ok {
 		if nb, ok := mesh["netbird"].(map[string]any); ok {
 			if ip, ok := nb["ip"].(string); ok && ip != "" {
 				return ip
 			}
+			// Seeds record the mesh name, not an address — ws:mac-mini
+			// carries only `fqdn`, which is why it resolved to nothing.
+			if fqdn, ok := nb["fqdn"].(string); ok && fqdn != "" {
+				return fqdn
+			}
 		}
 	}
 	if ip, ok := attrs["mesh_ip"].(string); ok && ip != "" {
 		return ip
 	}
+	for _, key := range []string{"host", "address", "public_host"} {
+		if v, ok := attrs[key].(string); ok && v != "" {
+			return v
+		}
+	}
 	return ""
 }
 
@@ -42,6 +544,13 @@ func resolveSSHUser(attrs map[string]any) string {
 			return u
 		}
 	}
+	// Workstations carry their login as a top-level `user` attribute
+	// (mac-mini: user: dtoro) rather than under ssh.user. Take it only when
+	// no explicit ssh.user was set, so a host that genuinely wants root still
+	// gets root.
+	if u, ok := attrs["user"].(string); ok && u != "" {
+		return u
+	}
 	return "root"
 }
 
@@ -57,148 +566,17 @@ func resolveSSHPort(attrs map[string]any) int {
 	return 22
 }
 
-func ForEntityType(entityType string, attrs map[string]any) []CheckDef {
-	host := ResolveHost(attrs)
-	user := resolveSSHUser(attrs)
-	port := resolveSSHPort(attrs)
-
-	ssh := func(script string) CheckDef {
-		return CheckDef{Kind: "ssh-script", Script: script, Host: host, User: user, Port: port}
-	}
-
-	switch entityType {
-	case "proxmox-host", "standalone-server":
-		if host == "" {
-			return nil
+// LogResult emits the one line that was missing: a type that asked for
+// monitoring and did not get it.
+func LogResult(slug, entityType string, res Result) {
+	switch {
+	case res.Undeclared:
+		slog.Info("checkdefaults: type declares no monitoring",
+			"entity", slug, "type", entityType)
+	case len(res.Skipped) > 0:
+		for _, s := range res.Skipped {
+			slog.Warn("checkdefaults: declared check not created",
+				"entity", slug, "type", entityType, "kind", s.Kind, "reason", s.Reason)
 		}
-		return []CheckDef{
-			{Kind: "ping", Host: host},
-			ssh("cpu_check.sh"),
-			ssh("memory_check.sh"),
-			ssh("load_check.sh"),
-			ssh("disk_usage_check.sh"),
-			ssh("updates_check.sh"),
-		}
-	case "workstation":
-		if host == "" {
-			return nil
-		}
-		return []CheckDef{
-			{Kind: "ping", Host: host},
-			ssh("cpu_check.sh"),
-			ssh("memory_check.sh"),
-			ssh("load_check.sh"),
-		}
-	case "lxc":
-		if host == "" {
-			return nil
-		}
-		return []CheckDef{
-			ssh("cpu_check.sh"),
-			ssh("memory_check.sh"),
-			ssh("load_check.sh"),
-			ssh("disk_usage_check.sh"),
-		}
-	case "vm":
-		if host == "" {
-			return nil
-		}
-		return []CheckDef{
-			{Kind: "ping", Host: host},
-		}
-	case "service":
-		if host == "" {
-			return nil
-		}
-		n, _ := attrs["name"].(string)
-		if n == "" {
-			return nil
-		}
-		return []CheckDef{
-			{Kind: "ssh-script", Script: "process_check.sh", Host: host, User: user, Port: port,
-				Extra: map[string]any{"args": n}},
-		}
-	}
-	return nil
-}
-
-func ShortSlug(slug string) string {
-	const n = 8
-	if len(slug) > n {
-		return slug[len(slug)-n:]
-	}
-	return slug
-}
-
-func DefaultInterval(kind string) int32 {
-	switch kind {
-	case "ping":
-		return 30
-	case "ssh-script":
-		return 60
-	default:
-		return 300
-	}
-}
-
-func Ensure(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, slug, entityType string, attrsJSON []byte) {
-	_, _ = tx.Exec(ctx,
-		`INSERT INTO entity_status (entity_id, health, updated_at)
-		 VALUES ($1, 'unknown', now())
-		 ON CONFLICT (entity_id) DO NOTHING`,
-		entityID)
-
-	var attrs map[string]any
-	if len(attrsJSON) > 0 {
-		json.Unmarshal(attrsJSON, &attrs)
-	}
-	if attrs == nil {
-		attrs = map[string]any{}
-	}
-
-	defs := ForEntityType(entityType, attrs)
-	if len(defs) == 0 {
-		return
-	}
-
-	for i, def := range defs {
-		checkID, err := uuid.NewV7()
-		if err != nil {
-			checkID = uuid.New()
-		}
-		checkSlug := fmt.Sprintf("check:%s:%s:%d", def.Kind, ShortSlug(slug), i)
-
-		_, _ = tx.Exec(ctx,
-			`INSERT INTO entities (id, slug, type, name, state, attributes, version, created_at, updated_at)
-			 VALUES ($1, $2, 'check', $2, 'active', '{}', 1, now(), now())
-			 ON CONFLICT (slug) DO NOTHING`,
-			checkID, checkSlug)
-
-		configMap := map[string]any{}
-		if def.Script != "" {
-			configMap["script"] = def.Script
-		}
-		if def.Host != "" {
-			configMap["host"] = def.Host
-		}
-		if def.User != "" && def.User != "root" {
-			configMap["user"] = def.User
-		}
-		if def.Port != 0 && def.Port != 22 {
-			configMap["port"] = def.Port
-		}
-		if def.Thresholds != nil {
-			configMap["thresholds"] = def.Thresholds
-		}
-		for k, v := range def.Extra {
-			configMap[k] = v
-		}
-		configJSON, _ := json.Marshal(configMap)
-
-		_, _ = tx.Exec(ctx,
-			`INSERT INTO check_defs (entity_id, target_id, kind, config, interval_s, timeout_s, enabled)
-			 VALUES ($1, $2, $3, $4, $5, 30, true)
-			 ON CONFLICT (entity_id) DO NOTHING`,
-			checkID, entityID, def.Kind, configJSON, DefaultInterval(def.Kind))
 	}
 }

internal/checkdefaults/defaults_test.go

@@ -0,0 +1,125 @@
+package checkdefaults
+
+import (
+	"testing"
+)
+
+// The attribute shapes here are copied from seeds/inventory.yaml. The original
+// resolveHost looked for lan_ip / mesh.netbird.ip / mesh_ip, none of which a
+// service or workstation actually carries — which is why 86 of 89 entities
+// ended up with no checks.
+func TestResolveHostAcceptsRealSeedShapes(t *testing.T) {
+	cases := []struct {
+		desc  string
+		attrs map[string]any
+		want  string
+	}{
+		{"lxc carries lan_ip", map[string]any{"lan_ip": "192.168.8.246"}, "192.168.8.246"},
+		{
+			"ws:mac-mini carries only a netbird fqdn",
+			map[string]any{"mesh": map[string]any{"netbird": map[string]any{
+				"fqdn": "mac-mini-234-17.netbird.selfhosted"}}},
+			"mac-mini-234-17.netbird.selfhosted",
+		},
+		{
+			"a netbird ip still wins over the fqdn",
+			map[string]any{"mesh": map[string]any{"netbird": map[string]any{
+				"ip": "100.122.0.10", "fqdn": "x.netbird.selfhosted"}}},
+			"100.122.0.10",
+		},
+		{"public_host as a last resort", map[string]any{"public_host": "media.hubris.network"}, "media.hubris.network"},
+		{"a service carries no address at all", map[string]any{
+			"url": "https://media.hubris.network", "port": 8096}, ""},
+		{"nil attrs", nil, ""},
+	}
+
+	for _, c := range cases {
+		if got := resolveHost(c.attrs); got != c.want {
+			t.Errorf("%s: resolveHost = %q, want %q", c.desc, got, c.want)
+		}
+	}
+}
+
+func TestHTTPURLPrefersAttributeThenName(t *testing.T) {
+	cases := []struct {
+		desc  string
+		name  string
+		attrs map[string]any
+		want  string
+	}{
+		{"explicit url wins", "jellyfin",
+			map[string]any{"url": "https://media.hubris.network"}, "https://media.hubris.network"},
+		{"public_host becomes https", "jellyfin",
+			map[string]any{"public_host": "media.hubris.network"}, "https://media.hubris.network"},
+		// Ingress routes carry the hostname as the entity name and usually
+		// declare no attributes at all.
+		{"hostname-shaped name", "media.hubris.network", nil, "https://media.hubris.network"},
+		{"a bare service name is not a hostname", "jellyfin", nil, ""},
+	}
+
+	for _, c := range cases {
+		got := httpURL(Target{Name: c.name}, c.attrs)
+		if got != c.want {
+			t.Errorf("%s: httpURL = %q, want %q", c.desc, got, c.want)
+		}
+	}
+}
+
+func TestBuildKindReportsWhyItSkipped(t *testing.T) {
+	// A declared kind that cannot be built must explain itself rather than
+	// vanish — that silence is what hid the coverage gap.
+	if defs, reason := buildKind(KindPing, Target{}, nil, "", "root", 22); len(defs) != 0 || reason == "" {
+		t.Errorf("ping without a host should skip with a reason, got %d defs / %q", len(defs), reason)
+	}
+	if defs, reason := buildKind(KindProcess, Target{Name: ""}, nil, "10.0.0.1", "root", 22); len(defs) != 0 || reason == "" {
+		t.Errorf("process without a name should skip with a reason, got %d defs / %q", len(defs), reason)
+	}
+	if defs, reason := buildKind("dns", Target{}, nil, "10.0.0.1", "root", 22); len(defs) != 0 || reason == "" {
+		t.Errorf("an unimplemented kind should skip with a reason, got %d defs / %q", len(defs), reason)
+	}
+}
+
+func TestBuildKindProcessPassesTheUnitName(t *testing.T) {
+	// process_check.sh reads $1 and answers "no service name provided"
+	// without it. checkdefaults always wrote args; nothing read them.
+	defs, reason := buildKind(KindProcess, Target{Name: "jellyfin"}, nil, "10.0.0.1", "root", 22)
+	if len(defs) != 1 {
+		t.Fatalf("expected one process check, got %d (%s)", len(defs), reason)
+	}
+	if got := defs[0].config["args"]; got != "jellyfin" {
+		t.Errorf("process check args = %v, want jellyfin", got)
+	}
+	if got := defs[0].config["script"]; got != "process_check.sh" {
+		t.Errorf("process check script = %v", got)
+	}
+}
+
+func TestBuildKindHTTPUsesAStatusRangeNotAnExactCode(t *testing.T) {
+	// Most services sit behind Authentik and answer 302/401.
+	defs, _ := buildKind(KindHTTP, Target{Name: "jellyfin"},
+		map[string]any{"url": "https://media.hubris.network"}, "", "root", 22)
+	if len(defs) != 1 {
+		t.Fatalf("expected one http check, got %d", len(defs))
+	}
+	if got := defs[0].config["max_status"]; got != 500 {
+		t.Errorf("max_status = %v, want 500", got)
+	}
+	if _, exact := defs[0].config["expected_status"]; exact {
+		t.Error("default http checks must not pin an exact status")
+	}
+}
+
+func TestBuildKindResourceExpandsToFourScripts(t *testing.T) {
+	defs, _ := buildKind(KindResource, Target{}, nil, "10.0.0.1", "root", 22)
+	if len(defs) != 4 {
+		t.Fatalf("resource should expand to 4 checks, got %d", len(defs))
+	}
+	for _, d := range defs {
+		if d.kind != "ssh-script" {
+			t.Errorf("resource check kind = %q, want ssh-script", d.kind)
+		}
+		if d.config["host"] != "10.0.0.1" {
+			t.Errorf("resource check lost its host: %v", d.config)
+		}
+	}
+}

internal/db/checks.go

@@ -0,0 +1,34 @@
+package db
+
+import (
+	"context"
+
+	"github.com/dtoro/oikos/internal/checkdefaults"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// EnsureEntityChecks derives an entity's default check_defs from the
+// monitoring spec of its type (resolving per-entity `monitoring` overrides).
+//
+// This is the single shared hook that keeps the check graph in sync with
+// entity mutations. Both the HTTP create/patch handlers and the MCP
+// entity-mutation tools (create_entity, update_entity_attributes) call it so
+// that flipping an entity's `monitoring` attribute regenerates checks
+// regardless of which surface made the change — previously only the HTTP
+// path ran check derivation, so entities mutated via MCP silently produced no
+// checks (see plans/2026-08-03-session-review-haos-monitoring-capability-gaps.md, A2).
+func EnsureEntityChecks(ctx context.Context, tx pgx.Tx, id uuid.UUID, slug, entityType, name string, attrs []byte) (checkdefaults.Result, error) {
+	tree, err := LoadTypeTree(ctx, tx)
+	if err != nil {
+		return checkdefaults.Result{}, err
+	}
+	res, err := checkdefaults.Ensure(ctx, tx, tree, checkdefaults.Target{
+		ID: id, Slug: slug, Type: entityType, Name: name, Attrs: attrs,
+	})
+	if err != nil {
+		return res, err
+	}
+	checkdefaults.LogResult(slug, entityType, res)
+	return res, nil
+}

internal/db/integration_test.go

@@ -167,6 +167,62 @@ func TestSeedIngestIdempotentAndNoDuplicateEdges(t *testing.T) {
 	}
 }
 
+// Regression: insertOneEntityType read tMap["attribute_schema"], but
+// seeds/ontology.yaml spells the key `attributes:`. The mismatch marshalled a
+// nil into the JSON literal `null` for every one of the 60 types, so no
+// attribute schema was ever ingested — the API and `oikos export` returned
+// null across the board, silently, for the life of the project.
+func TestSeedIngestsAttributeSchemas(t *testing.T) {
+	pool := newTestPool(t)
+	seedAll(t, pool, seedsDir())
+
+	if n := count(t, pool,
+		`SELECT count(*) FROM entity_types WHERE attribute_schema = 'null'::jsonb`); n != 0 {
+		t.Errorf("%d entity types stored the JSON literal null instead of a schema or SQL NULL", n)
+	}
+
+	if n := count(t, pool,
+		`SELECT count(*) FROM entity_types WHERE jsonb_typeof(attribute_schema) = 'object'`); n == 0 {
+		t.Fatal("no entity type ingested an attribute schema")
+	}
+
+	// A type declaring `attributes:` must round-trip its properties.
+	if n := count(t, pool, `SELECT count(*) FROM entity_types
+		WHERE name = 'lxc' AND attribute_schema #>> '{properties,pve_id,type}' = 'integer'`); n != 1 {
+		t.Error("lxc.attribute_schema lost its declared pve_id property")
+	}
+
+	// A type declaring none stores SQL NULL, not a JSON null.
+	if n := count(t, pool, `SELECT count(*) FROM entity_types
+		WHERE name = 'sensor' AND attribute_schema IS NULL`); n != 1 {
+		t.Error("a type declaring no attributes should store SQL NULL")
+	}
+}
+
+// monitoring_spec drives which entities coverageSweep may flag as unmonitored,
+// so the three states have to survive ingest distinctly: SQL NULL (undeclared,
+// resolved from an ancestor or the layer default), '[]' (explicitly
+// unmonitorable), and a non-empty array (the kinds the type warrants).
+func TestSeedIngestsMonitoringSpec(t *testing.T) {
+	pool := newTestPool(t)
+	seedAll(t, pool, seedsDir())
+
+	cases := []struct {
+		typ, where, desc string
+	}{
+		{"service", `monitoring_spec = '["http","process"]'::jsonb`, "declared kinds"},
+		{"machine", `monitoring_spec = '["ping","resource","updates"]'::jsonb`, "declared on an abstract type"},
+		{"site", `monitoring_spec = '[]'::jsonb`, "explicitly unmonitorable"},
+		{"lxc", `monitoring_spec IS NULL`, "inherits from container, so its own column is NULL"},
+	}
+	for _, c := range cases {
+		if n := count(t, pool, fmt.Sprintf(
+			`SELECT count(*) FROM entity_types WHERE name = '%s' AND %s`, c.typ, c.where)); n != 1 {
+			t.Errorf("%s (%s): monitoring_spec did not match %s", c.typ, c.desc, c.where)
+		}
+	}
+}
+
 func TestAbstractTypeRejected(t *testing.T) {
 	pool := newTestPool(t)
 	seedAll(t, pool, seedsDir())
@@ -250,7 +306,17 @@ func TestBlastRadiusTerminatesOnCycles(t *testing.T) {
 	pool := newTestPool(t)
 	seedAll(t, pool, seedsDir())
 
-	// Build a dependency cycle: gitea → caddy → authentik → gitea
+	// Build a dependency cycle: gitea → caddy → authentik → gitea.
+	//
+	// `depends-on` is declared blast_direction: backward — "A depends-on B"
+	// means B failing breaks A — so the blast radius of gitea walks the edges
+	// BACKWARDS: whoever depends on gitea is affected first. That is authentik
+	// (1 hop), then caddy which depends on authentik (2 hops).
+	//
+	// This test previously asserted caddy=1, authentik=2, which is the same
+	// cycle walked the wrong way round: blast_radius used to follow every edge
+	// source→target regardless of what the edge means, so it answered "what
+	// does gitea depend on" while being named for the opposite question.
 	cycle := []byte(`
 version: 1
 relationships:
@@ -286,14 +352,24 @@ relationships:
 		}
 		got[slug] = depth
 	}
-	want := map[string]int{"service:gitea": 0, "service:caddy": 1, "service:authentik": 2}
+	want := map[string]int{"service:gitea": 0, "service:authentik": 1, "service:caddy": 2}
 	for slug, depth := range want {
 		if got[slug] != depth {
 			t.Errorf("blast_radius[%s] = %d, want %d (full: %v)", slug, got[slug], depth, got)
 		}
 	}
-	if len(got) != len(want) {
-		t.Errorf("blast_radius returned %d nodes, want %d: %v", len(got), len(want), got)
+	// Deliberately not an exact node count. Walking the right way round also
+	// surfaces the real seed's own dependents of gitea (homelab-mcp and what
+	// depends on it), which are correct answers — the old exact-count
+	// assertion only held because the forward walk found nothing real.
+	// What matters here is that the cycle terminates rather than recursing.
+	if len(got) > 20 {
+		t.Errorf("blast_radius did not terminate sensibly: %d nodes: %v", len(got), got)
+	}
+	for slug, depth := range got {
+		if depth > 5 {
+			t.Errorf("blast_radius[%s] = %d, beyond the max_depth bound", slug, depth)
+		}
 	}
 }
 

internal/db/lifecycle.go

@@ -0,0 +1,146 @@
+package db
+
+import (
+	"context"
+	"encoding/json"
+	"errors"
+	"fmt"
+	"strings"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// ErrTransitionInvalid is a sentinel returned by ValidateTransition when the
+// from→to pair is not a declared lifecycle transition or a precondition fails.
+// Callers test with errors.Is to distinguish semantic validation failures
+// (→ HTTP 409) from infrastructure errors (→ HTTP 500).
+var ErrTransitionInvalid = errors.New("invalid lifecycle transition")
+
+// ValidateTransition enforces an entity type's lifecycle: fromState → toState
+// must be a declared transition, and every precondition it lists must hold. A
+// type with no lifecycle defined allows any state. A no-op (fromState ==
+// toState) passes immediately.
+//
+// Shared by the HTTP PATCH path and the MCP set_entity_state tool so both
+// surfaces apply identical lifecycle rules — previously only the HTTP path
+// validated transitions, so an agent changing state via MCP could skip the
+// graph's retire/deprecate guardrails entirely.
+func ValidateTransition(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, entityType, fromState, toState string) error {
+	if toState == fromState {
+		return nil
+	}
+	lc, err := sqlcgen.New(tx).GetLifecycleForType(ctx, entityType)
+	if err != nil {
+		if err == pgx.ErrNoRows {
+			return nil // no lifecycle defined → any state allowed
+		}
+		return err
+	}
+	var transitions map[string]map[string]json.RawMessage
+	if err := json.Unmarshal(lc.Transitions, &transitions); err != nil {
+		return fmt.Errorf("parse lifecycle transitions: %w", err)
+	}
+	tos, ok := transitions[fromState]
+	if !ok {
+		return fmt.Errorf("%w: no transitions defined from %q", ErrTransitionInvalid, fromState)
+	}
+	trans, ok := tos[toState]
+	if !ok {
+		return fmt.Errorf("%w: %s → %s is not a declared lifecycle transition", ErrTransitionInvalid, fromState, toState)
+	}
+	var gate struct {
+		Requires []string `json:"requires"`
+	}
+	if err := json.Unmarshal(trans, &gate); err == nil {
+		for _, check := range gate.Requires {
+			if err := checkPrecondition(ctx, tx, entityID, entityType, check); err != nil {
+				return fmt.Errorf("%w: precondition %q not met: %w", ErrTransitionInvalid, check, err)
+			}
+		}
+	}
+	return nil
+}
+
+// checkPrecondition evaluates one mechanical precondition named by a lifecycle
+// transition's `requires` list. Soft/operator-confirmed checks pass; unknown
+// checks are skipped (operator intent overrides). Moved here from httpapi so
+// both surfaces share one implementation.
+func checkPrecondition(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, entityType, check string) error {
+	switch check {
+	case "no-inbound-edges":
+		var count int
+		if err := tx.QueryRow(ctx,
+			"SELECT count(*) FROM relationships WHERE target_id = $1 AND valid_to IS NULL", entityID).Scan(&count); err != nil {
+			return err
+		}
+		if count > 0 {
+			return fmt.Errorf("%d inbound relationship edges remaining", count)
+		}
+	case "backups-verified", "secrets-revoked", "ingress-dns-removed":
+		var attrs string
+		if err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs); err != nil {
+			return err
+		}
+		want := map[string]string{
+			"backups-verified":   "backups_verified",
+			"secrets-revoked":    "secrets_revoked",
+			"ingress-dns-removed": "ingress_dns_removed",
+		}[check]
+		if !strings.Contains(attrs, want) {
+			return fmt.Errorf("%s not recorded in entity attributes", want)
+		}
+	case "age-key-enrolled-if-needed":
+		if entityType == "workstation" {
+			var attrs string
+			if err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs); err != nil {
+				return err
+			}
+			if !strings.Contains(attrs, "age_pubkey") {
+				return fmt.Errorf("age key not enrolled (no age_pubkey in attributes)")
+			}
+		}
+	case "mesh-joined-if-needed":
+		if entityType == "workstation" {
+			var attrs string
+			if err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs); err != nil {
+				return err
+			}
+			if !strings.Contains(attrs, "mesh_ip") {
+				return fmt.Errorf("mesh not joined (no mesh_ip in attributes)")
+			}
+		}
+	case "health-check-answering":
+		st, err := sqlcgen.New(tx).GetEntityStatus(ctx, entityID)
+		if err != nil || st.Health == "unknown" || st.Health == "down" {
+			h := "unknown"
+			if err == nil {
+				h = st.Health
+			}
+			return fmt.Errorf("health check not answering (status: %s)", h)
+		}
+	case "doc-page-complete":
+		var count int
+		if err := tx.QueryRow(ctx, `
+			SELECT count(*) FROM relationships r
+			JOIN entities ke ON ke.id = r.source_id
+			WHERE r.target_id = $1 AND r.valid_to IS NULL
+			  AND r.type = 'documents' AND ke.type IN ('document','runbook','investigation')`,
+			entityID).Scan(&count); err != nil {
+			return err
+		}
+		if count == 0 {
+			return fmt.Errorf("no documentation linked to entity")
+		}
+	case "inventory-entry", "ip-reserved", "storage-pool-chosen", "cancelled-note",
+		"preflight-passed", "error-summary", "replacement-live-or-role-retired",
+		"replacement-failed", "post-verify-passed", "recovery-verified", "written-off",
+		"ingress-live-if-public", "doc-page-stub", "un-deprecate-note", "write-off-note":
+		// Soft checks — always pass. Operator-confirmed via the transition
+		// request itself, or not mechanically enforceable.
+	default:
+		// Unknown preconditions are skipped (operator intent overrides).
+	}
+	return nil
+}

internal/db/queries/entities.sql

@@ -27,9 +27,6 @@ WHERE e.type IN (SELECT name FROM tt)
 ORDER BY e.slug
 LIMIT sqlc.arg('lim');
 
--- name: ListEntitiesCapped :many
-SELECT e.* FROM entities e ORDER BY e.slug LIMIT $1;
-
 -- name: InsertEntity :one
 INSERT INTO entities (id, slug, type, name, state, attributes)
 VALUES ($1, $2, $3, $4, $5, $6)

internal/db/queries/operations.sql

@@ -14,11 +14,6 @@ WHERE (sqlc.narg('state')::text IS NULL OR sig.state = sqlc.narg('state'))
 ORDER BY se.slug
 LIMIT sqlc.arg('lim');
 
--- name: ListEntityStatus :many
-SELECT e.slug, e.type, st.health, st.last_check_at
-FROM entity_status st JOIN entities e ON e.id = st.entity_id
-ORDER BY e.slug;
-
 -- name: GetIdempotentResponse :one
 SELECT response_code, response_body, request_hash FROM idempotency_keys
 WHERE actor = $1 AND key = $2;
@@ -30,8 +25,8 @@ ON CONFLICT (actor, key) DO NOTHING;
 
 -- name: InsertAuditEntry :exec
 INSERT INTO audit_log (actor_type, actor_id, action, entity_id, method, path,
-                       status_code, detail, source_ip, correlation_id)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10);
+                       status_code, detail, source_ip, correlation_id, session_id)
+VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11);
 
 -- name: InsertEvent :one
 INSERT INTO events (type, entity_id, severity, source, data, correlation_id)
@@ -60,12 +55,36 @@ FROM events WHERE id > $1 ORDER BY id ASC LIMIT $2;
 -- =====================================================================
 
 -- name: ListEnabledCheckDefs :many
+-- Enabled AND due. interval_s used to be selected but never filtered on, so
+-- every check ran on every 30s pass and the declared intervals meant nothing.
+-- NULL last_run_at = never run = due now.
 SELECT cd.entity_id, cd.target_id, cd.target_type, cd.kind, cd.config,
        cd.interval_s, cd.timeout_s, cd.zone, cd.enabled, cd.updated_at,
        e.slug AS entity_slug
 FROM check_defs cd
 JOIN entities e ON e.id = cd.entity_id
-WHERE cd.enabled = true;
+LEFT JOIN entities tgt ON tgt.id = cd.target_id
+WHERE cd.enabled = true
+  AND (tgt.id IS NULL OR tgt.state IS NULL OR tgt.state NOT IN ('deprecated', 'destroyed'))
+  AND (cd.last_run_at IS NULL
+       OR cd.last_run_at <= now() - make_interval(secs => cd.interval_s));
+
+-- name: MarkCheckRun :exec
+UPDATE check_defs SET last_run_at = now(), last_health = $2 WHERE entity_id = $1;
+
+-- name: WorstHealthForTarget :one
+-- An entity is as healthy as its unhealthiest check. Checks that have not run
+-- yet (last_health IS NULL) are ignored rather than counted as unknown, so a
+-- newly added check does not drag a known-good entity down before it has
+-- produced a verdict.
+SELECT COALESCE(
+  (SELECT last_health FROM check_defs
+   WHERE enabled AND target_id = $1 AND last_health IS NOT NULL
+   ORDER BY CASE last_health
+     WHEN 'down' THEN 0 WHEN 'degraded' THEN 1 WHEN 'stale' THEN 2
+     WHEN 'unknown' THEN 3 ELSE 4 END
+   LIMIT 1),
+  'unknown')::text AS health;
 
 -- name: GetCheckDef :one
 SELECT * FROM check_defs WHERE entity_id = $1;
@@ -89,9 +108,6 @@ DO UPDATE SET occurrence_count = signals.occurrence_count + 1,
               updated_at = now()
 RETURNING *;
 
--- name: UpdateSignalState :exec
-UPDATE signals SET state = $2, updated_at = now() WHERE entity_id = $1;
-
 -- name: GetOpenSignalsForAutoAct :many
 -- Signals with auto-act classifications that haven't been executed yet
 SELECT s.*, c.entity_id AS classification_id, c.action, c.risk_class, c.route,
@@ -106,12 +122,6 @@ WHERE c.route = 'auto-act'
 ORDER BY s.last_seen_at ASC
 LIMIT $1;
 
--- name: InsertClassification :exec
-INSERT INTO classifications (entity_id, signal_entity_id, target_entity_id, action,
-    recommended_action, risk_class, route, blast_radius, pattern_confidence,
-    skill_id, autonomy_check, reasoning, correlation_id)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13);
-
 -- name: ListClassifications :many
 SELECT c.entity_id, c.signal_entity_id, c.target_entity_id, c.action,
        c.recommended_action, c.risk_class, c.route, c.blast_radius,
@@ -153,11 +163,6 @@ WHERE (sqlc.narg('status')::text IS NULL OR e.status = sqlc.narg('status'))
 ORDER BY te.slug
 LIMIT sqlc.arg('lim');
 
--- name: InsertFeedback :exec
-INSERT INTO feedback (entity_id, execution_id, outcome, observation, lesson,
-    unexpected_side_effects, tags)
-VALUES ($1, $2, $3, $4, $5, $6, $7);
-
 -- name: GetFeedbackAfterWatermark :many
 SELECT f.entity_id, f.execution_id, f.outcome, f.observation, f.lesson,
        f.unexpected_side_effects, f.tags, f.created_at,
@@ -201,11 +206,6 @@ SELECT * FROM skills
 WHERE (sqlc.narg('status')::text IS NULL OR status = sqlc.narg('status'))
 ORDER BY name, version DESC;
 
--- name: InsertSkill :exec
-INSERT INTO skills (entity_id, version, name, procedure, applies_type, action,
-    pattern_ids, status, changed_by, change_reason)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10);
-
 -- name: UpdateSkillStatus :exec
 UPDATE skills SET status = $2, last_used_at = now() WHERE entity_id = $1 AND version = $2;
 

internal/db/queries/relationships.sql

@@ -22,12 +22,6 @@ WHERE r.valid_to IS NULL
   AND (sqlc.narg('rel_types')::text[] IS NULL OR r.type = ANY(sqlc.narg('rel_types')::text[]))
 ORDER BY r.type, se.slug, te.slug;
 
--- name: UpsertCurrentRelationship :exec
-INSERT INTO relationships (source_id, target_id, type, attributes, valid_from, valid_to)
-VALUES ($1, $2, $3, $4, now(), NULL)
-ON CONFLICT (source_id, target_id, type) WHERE valid_to IS NULL
-DO UPDATE SET attributes = EXCLUDED.attributes;
-
 -- name: EndCurrentRelationship :execrows
 UPDATE relationships SET valid_to = now()
 WHERE source_id = $1 AND target_id = $2 AND type = $3 AND valid_to IS NULL;

internal/db/seed.go

@@ -13,14 +13,15 @@ import (
 
 // SeedResult holds counts from a seed ingest operation.
 type SeedResult struct {
-	Lifecycles       int
-	EntityTypes      int
+	Lifecycles        int
+	EntityTypes       int
 	RelationshipTypes int
-	Entities         int
-	Relationships    int
-	RiskClasses      int
-	ApprovalRules    int
-	AutonomySettings int
+	Entities          int
+	Relationships     int
+	RiskClasses       int
+	ApprovalRules     int
+	AutonomySettings  int
+	Checks            int
 }
 
 // IngestOntologySeed ingests seeds/ontology.yaml into the DB.
@@ -66,12 +67,20 @@ func IngestOntologySeed(ctx context.Context, tx pgx.Tx, data map[string]any) (*S
 		targetType, _ := rtMap["target"].(string)
 		cardinality, _ := rtMap["cardinality"].(string)
 		desc, _ := rtMap["description"].(string)
+		// Which end of the edge depends on the other; drives blast_radius().
+		// Absent means 'none' — an undeclared edge contributes nothing rather
+		// than silently producing a wrong dependency answer.
+		blastDirection, _ := rtMap["blast_direction"].(string)
+		if blastDirection == "" {
+			blastDirection = "none"
+		}
 		_, err := tx.Exec(ctx,
-			`INSERT INTO relationship_types (name, inverse, source_type, target_type, cardinality, description)
-			 VALUES ($1, $2, $3, $4, $5, $6)
+			`INSERT INTO relationship_types (name, inverse, source_type, target_type, cardinality, description, blast_direction)
+			 VALUES ($1, $2, $3, $4, $5, $6, $7)
 			 ON CONFLICT (name) DO UPDATE SET inverse = $2, source_type = $3,
-			   target_type = $4, cardinality = $5, description = $6`,
-			name, nullableStr(inverse), sourceType, targetType, cardinality, desc)
+			   target_type = $4, cardinality = $5, description = $6,
+			   blast_direction = $7`,
+			name, nullableStr(inverse), sourceType, targetType, cardinality, desc, blastDirection)
 		if err != nil {
 			return nil, fmt.Errorf("relationship_type %s: %w", name, err)
 		}
@@ -96,6 +105,7 @@ func IngestInventorySeed(ctx context.Context, tx pgx.Tx, data map[string]any) (*
 	// Entities
 	entities, _ := data["entities"].([]any)
 	entityTypes := make(map[string]string) // slug -> type, for edge validation
+	var pendingChecks []checkdefaults.Target
 	for _, raw := range entities {
 		eMap, ok := raw.(map[string]any)
 		if !ok {
@@ -144,7 +154,12 @@ func IngestInventorySeed(ctx context.Context, tx pgx.Tx, data map[string]any) (*
 			return nil, fmt.Errorf("entity_status %s: %w", slug, err)
 		}
 
-		checkdefaults.Ensure(ctx, tx, entityID, slug, typeName, attrsBytes)
+		// Default checks are deferred until after relationships are ingested:
+		// a service has no address of its own and inherits its container's,
+		// which means the hosting edge has to exist first.
+		pendingChecks = append(pendingChecks, checkdefaults.Target{
+			ID: entityID, Slug: slug, Type: typeName, Name: name, Attrs: attrsBytes,
+		})
 
 		r.Entities++
 	}
@@ -208,6 +223,19 @@ func IngestInventorySeed(ctx context.Context, tx pgx.Tx, data map[string]any) (*
 		return nil, err
 	}
 
+	// Default checks, now that hosting edges exist. Errors here are fatal:
+	// swallowing them is what let a foreign-key violation abort the ingest
+	// transaction while surfacing as an unrelated failure several entities
+	// later.
+	for _, target := range pendingChecks {
+		res, err := checkdefaults.Ensure(ctx, tx, tree, target)
+		if err != nil {
+			return nil, fmt.Errorf("default checks for %s: %w", target.Slug, err)
+		}
+		checkdefaults.LogResult(target.Slug, target.Type, res)
+		r.Checks += res.Created
+	}
+
 	return r, nil
 }
 
@@ -361,19 +389,68 @@ func insertOneEntityType(ctx context.Context, tx pgx.Tx, name string, tMap map[s
 	layer, _ := tMap["layer"].(string)
 	desc, _ := tMap["description"].(string)
 	lifecycleID, _ := tMap["lifecycle"].(string)
-	attrSchema := tMap["attribute_schema"]
 
-	schemaBytes, _ := json.Marshal(attrSchema)
+	// seeds/ontology.yaml spells this `attributes:`. Reading it as
+	// "attribute_schema" silently marshalled nil to the JSON literal `null`
+	// for every type, so no attribute schema was ever ingested — the API and
+	// `oikos export` returned null for all 60 types.
+	attrSchema := tMap["attributes"]
 	_, err := tx.Exec(ctx,
 		`INSERT INTO entity_types (name, parent_type, is_abstract, domain, layer, description,
-		     lifecycle_id, attribute_schema, schema_version, status, created_at, updated_at)
-		 VALUES ($1, $2, $3, $4, $5, $6, $7, $8, 1, 'active', now(), now())
+		     lifecycle_id, attribute_schema, monitoring_spec, schema_version, status, created_at, updated_at)
+		 VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, 1, 'active', now(), now())
 		 ON CONFLICT (name) DO UPDATE SET parent_type = $2, is_abstract = $3, domain = $4,
-		   layer = $5, description = $6, lifecycle_id = $7, attribute_schema = $8, updated_at = now()`,
-		name, nullableStr(parent), isAbstract, domain, layer, desc, nullableStr(lifecycleID), nullableStr(string(schemaBytes)))
+		   layer = $5, description = $6, lifecycle_id = $7, attribute_schema = $8,
+		   monitoring_spec = $9, updated_at = now()`,
+		name, nullableStr(parent), isAbstract, domain, layer, desc, nullableStr(lifecycleID),
+		attributeSchemaJSON(attrSchema), monitoringSpecJSON(tMap["monitoring"]))
 	return err
 }
 
+// attributeSchemaJSON marshals a type's `attributes:` block for storage,
+// mapping "the type declares no schema" to SQL NULL rather than to the JSON
+// literal `null`. Both readers already treat a JSON `null` as absent, but a
+// real NULL is what `attribute_schema IS NULL` expects and is what the column
+// meant all along.
+func attributeSchemaJSON(v any) any {
+	if v == nil {
+		return nil
+	}
+	b, err := json.Marshal(v)
+	if err != nil {
+		return nil
+	}
+	return string(b)
+}
+
+// monitoringSpecJSON normalises an entity type's `monitoring:` declaration into
+// the JSONB stored in entity_types.monitoring_spec. Three outcomes, and the
+// difference between the last two is load-bearing for coverage signalling:
+//
+//	absent          → nil   (SQL NULL) — undeclared, an ontology gap
+//	none | []       → "[]"            — explicitly unmonitorable, by design
+//	[http, resource]→ '["http","resource"]'
+//
+// `monitoring: none` is accepted as a more legible spelling of `[]`; YAML
+// parses the bare word as the string "none", not as null.
+func monitoringSpecJSON(v any) any {
+	switch spec := v.(type) {
+	case nil:
+		return nil
+	case string:
+		if spec == "none" {
+			return "[]"
+		}
+		// A single kind written unquoted, e.g. `monitoring: http`.
+		b, _ := json.Marshal([]string{spec})
+		return string(b)
+	case []any:
+		b, _ := json.Marshal(toStringSlice(spec))
+		return string(b)
+	}
+	return nil
+}
+
 func toStringSlice(v any) []string {
 	if v == nil {
 		return nil
@@ -407,4 +484,3 @@ func keysOf(m map[string]map[string]any) []string {
 	}
 	return keys
 }
-

internal/db/sqlcgen/entities.sql.go

@@ -177,43 +177,6 @@ func (q *Queries) ListEntities(ctx context.Context, arg ListEntitiesParams) ([]E
 	return items, nil
 }
 
-const listEntitiesCapped = `-- name: ListEntitiesCapped :many
-SELECT e.id, e.slug, e.type, e.name, e.state, e.attributes, e.maintenance_until, e.version, e.created_at, e.updated_at, e.enrolled_at, e.enrolled_by FROM entities e ORDER BY e.slug LIMIT $1
-`
-
-func (q *Queries) ListEntitiesCapped(ctx context.Context, limit int32) ([]Entity, error) {
-	rows, err := q.db.Query(ctx, listEntitiesCapped, limit)
-	if err != nil {
-		return nil, err
-	}
-	defer rows.Close()
-	var items []Entity
-	for rows.Next() {
-		var i Entity
-		if err := rows.Scan(
-			&i.ID,
-			&i.Slug,
-			&i.Type,
-			&i.Name,
-			&i.State,
-			&i.Attributes,
-			&i.MaintenanceUntil,
-			&i.Version,
-			&i.CreatedAt,
-			&i.UpdatedAt,
-			&i.EnrolledAt,
-			&i.EnrolledBy,
-		); err != nil {
-			return nil, err
-		}
-		items = append(items, i)
-	}
-	if err := rows.Err(); err != nil {
-		return nil, err
-	}
-	return items, nil
-}
-
 const updateEntity = `-- name: UpdateEntity :one
 UPDATE entities SET
     name = COALESCE($1, name),

internal/db/sqlcgen/models.go

@@ -35,11 +35,19 @@ type AgentMessage struct {
 }
 
 type AgentSession struct {
-	ID           uuid.UUID
-	Title        string
-	Actor        string
-	CreatedAt    time.Time
-	LastActiveAt time.Time
+	ID               uuid.UUID
+	Title            string
+	Actor            string
+	CreatedAt        time.Time
+	LastActiveAt     time.Time
+	Goal             string
+	Status           string
+	Outcome          *string
+	Summary          string
+	EntityID         *uuid.UUID
+	CompletionNudges int32
+	Blocker          string
+	ClosedAt         *time.Time
 }
 
 type Approval struct {
@@ -83,6 +91,7 @@ type AuditLog struct {
 	Detail        []byte
 	SourceIp      *string
 	CorrelationID *string
+	SessionID     *uuid.UUID
 }
 
 type AutonomySetting struct {
@@ -103,6 +112,10 @@ type CheckDef struct {
 	Zone       *string
 	Enabled    bool
 	UpdatedAt  time.Time
+	// When this check last executed. NULL = never, due immediately. Compared against interval_s to decide due-ness.
+	LastRunAt *time.Time
+	// This check's own most recent verdict (healthy/degraded/down/unknown). entity_status.health is the worst of these across the target's enabled checks.
+	LastHealth *string
 }
 
 type Classification struct {
@@ -170,6 +183,8 @@ type EntityType struct {
 	Status          string
 	CreatedAt       time.Time
 	UpdatedAt       time.Time
+	// Check kinds this type warrants, resolved through parent_type. NULL means undeclared (an ontology gap), [] means explicitly unmonitorable, ["http","resource"] means declared kinds. Populated from seeds/ontology.yaml.
+	MonitoringSpec []byte
 }
 
 type Event struct {
@@ -204,6 +219,14 @@ type Execution struct {
 	CreatedAt        time.Time
 }
 
+type ExecutionLog struct {
+	ExecutionID uuid.UUID
+	Ts          time.Time
+	Seq         int32
+	Stream      string
+	Chunk       string
+}
+
 type Feedback struct {
 	EntityID              uuid.UUID
 	ExecutionID           uuid.UUID
@@ -234,6 +257,20 @@ type KnowledgeEntity struct {
 	UpdatedAt   time.Time
 	ContentHash *string
 	Search      interface{}
+	EditedBy    string
+	DeletedAt   *time.Time
+}
+
+type KnowledgeRevision struct {
+	ID        int64
+	EntityID  uuid.UUID
+	Title     string
+	Content   string
+	Source    *string
+	Tags      []string
+	EditedBy  string
+	VersionAt time.Time
+	RevisedAt time.Time
 }
 
 type Ledger struct {
@@ -289,6 +326,13 @@ type MetricSample struct {
 	Tags     []byte
 }
 
+type NomosPlanExecution struct {
+	ExecutionID uuid.UUID
+	SessionID   uuid.UUID
+	ContinuedAt *time.Time
+	CreatedAt   time.Time
+}
+
 type Pattern struct {
 	EntityID        uuid.UUID
 	AppliesType     string
@@ -336,6 +380,8 @@ type RelationshipType struct {
 	Cardinality string
 	Description *string
 	CreatedAt   time.Time
+	// Which end of this edge depends on the other. forward = target depends on source. backward = source depends on target. none = no runtime dependency. Drives blast_radius().
+	BlastDirection string
 }
 
 type RiskClass struct {
@@ -351,6 +397,33 @@ type SeedVersion struct {
 	AppliedAt   time.Time
 }
 
+type SessionPlanStep struct {
+	ID             uuid.UUID
+	SessionID      uuid.UUID
+	Seq            int32
+	Title          string
+	Detail         string
+	Status         string
+	ExecutionID    *uuid.UUID
+	TargetSlug     *string
+	StartedAt      *time.Time
+	FinishedAt     *time.Time
+	CreatedAt      time.Time
+	Generation     int32
+	ReplacedReason *string
+}
+
+type SessionQuestion struct {
+	ID         uuid.UUID
+	SessionID  uuid.UUID
+	Prompt     string
+	Context    []byte
+	Status     string
+	Answer     *string
+	CreatedAt  time.Time
+	AnsweredAt *time.Time
+}
+
 type Signal struct {
 	EntityID        uuid.UUID
 	Kind            string

internal/db/sqlcgen/ontology.sql.go

@@ -30,7 +30,7 @@ func (q *Queries) GetLifecycleForType(ctx context.Context, name string) (Lifecyc
 }
 
 const listEntityTypes = `-- name: ListEntityTypes :many
-SELECT name, parent_type, is_abstract, domain, layer, description, lifecycle_id, attribute_schema, schema_version, status, created_at, updated_at FROM entity_types ORDER BY name
+SELECT name, parent_type, is_abstract, domain, layer, description, lifecycle_id, attribute_schema, schema_version, status, created_at, updated_at, monitoring_spec FROM entity_types ORDER BY name
 `
 
 func (q *Queries) ListEntityTypes(ctx context.Context) ([]EntityType, error) {
@@ -55,6 +55,7 @@ func (q *Queries) ListEntityTypes(ctx context.Context) ([]EntityType, error) {
 			&i.Status,
 			&i.CreatedAt,
 			&i.UpdatedAt,
+			&i.MonitoringSpec,
 		); err != nil {
 			return nil, err
 		}
@@ -98,7 +99,7 @@ func (q *Queries) ListLifecycleDefs(ctx context.Context) ([]LifecycleDef, error)
 }
 
 const listRelationshipTypes = `-- name: ListRelationshipTypes :many
-SELECT name, inverse, source_type, target_type, cardinality, description, created_at FROM relationship_types ORDER BY name
+SELECT name, inverse, source_type, target_type, cardinality, description, created_at, blast_direction FROM relationship_types ORDER BY name
 `
 
 func (q *Queries) ListRelationshipTypes(ctx context.Context) ([]RelationshipType, error) {
@@ -118,6 +119,7 @@ func (q *Queries) ListRelationshipTypes(ctx context.Context) ([]RelationshipType
 			&i.Cardinality,
 			&i.Description,
 			&i.CreatedAt,
+			&i.BlastDirection,
 		); err != nil {
 			return nil, err
 		}

internal/db/sqlcgen/operations.sql.go

@@ -51,7 +51,7 @@ func (q *Queries) GetAutonomySetting(ctx context.Context, key string) (string, e
 }
 
 const getCheckDef = `-- name: GetCheckDef :one
-SELECT entity_id, target_id, target_type, kind, config, interval_s, timeout_s, zone, enabled, updated_at FROM check_defs WHERE entity_id = $1
+SELECT entity_id, target_id, target_type, kind, config, interval_s, timeout_s, zone, enabled, updated_at, last_run_at, last_health FROM check_defs WHERE entity_id = $1
 `
 
 func (q *Queries) GetCheckDef(ctx context.Context, entityID uuid.UUID) (CheckDef, error) {
@@ -68,6 +68,8 @@ func (q *Queries) GetCheckDef(ctx context.Context, entityID uuid.UUID) (CheckDef
 		&i.Zone,
 		&i.Enabled,
 		&i.UpdatedAt,
+		&i.LastRunAt,
+		&i.LastHealth,
 	)
 	return i, err
 }
@@ -351,8 +353,8 @@ func (q *Queries) InsertApproval(ctx context.Context, arg InsertApprovalParams)
 
 const insertAuditEntry = `-- name: InsertAuditEntry :exec
 INSERT INTO audit_log (actor_type, actor_id, action, entity_id, method, path,
-                       status_code, detail, source_ip, correlation_id)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)
+                       status_code, detail, source_ip, correlation_id, session_id)
+VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11)
 `
 
 type InsertAuditEntryParams struct {
@@ -366,6 +368,7 @@ type InsertAuditEntryParams struct {
 	Detail        []byte
 	SourceIp      *string
 	CorrelationID *string
+	SessionID     *uuid.UUID
 }
 
 func (q *Queries) InsertAuditEntry(ctx context.Context, arg InsertAuditEntryParams) error {
@@ -380,6 +383,7 @@ func (q *Queries) InsertAuditEntry(ctx context.Context, arg InsertAuditEntryPara
 		arg.Detail,
 		arg.SourceIp,
 		arg.CorrelationID,
+		arg.SessionID,
 	)
 	return err
 }
@@ -416,48 +420,6 @@ func (q *Queries) InsertCheckDef(ctx context.Context, arg InsertCheckDefParams)
 	return err
 }
 
-const insertClassification = `-- name: InsertClassification :exec
-INSERT INTO classifications (entity_id, signal_entity_id, target_entity_id, action,
-    recommended_action, risk_class, route, blast_radius, pattern_confidence,
-    skill_id, autonomy_check, reasoning, correlation_id)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10, $11, $12, $13)
-`
-
-type InsertClassificationParams struct {
-	EntityID          uuid.UUID
-	SignalEntityID    *uuid.UUID
-	TargetEntityID    *uuid.UUID
-	Action            string
-	RecommendedAction []byte
-	RiskClass         string
-	Route             string
-	BlastRadius       []uuid.UUID
-	PatternConfidence *float32
-	SkillID           *uuid.UUID
-	AutonomyCheck     *string
-	Reasoning         []byte
-	CorrelationID     string
-}
-
-func (q *Queries) InsertClassification(ctx context.Context, arg InsertClassificationParams) error {
-	_, err := q.db.Exec(ctx, insertClassification,
-		arg.EntityID,
-		arg.SignalEntityID,
-		arg.TargetEntityID,
-		arg.Action,
-		arg.RecommendedAction,
-		arg.RiskClass,
-		arg.Route,
-		arg.BlastRadius,
-		arg.PatternConfidence,
-		arg.SkillID,
-		arg.AutonomyCheck,
-		arg.Reasoning,
-		arg.CorrelationID,
-	)
-	return err
-}
-
 const insertEvent = `-- name: InsertEvent :one
 INSERT INTO events (type, entity_id, severity, source, data, correlation_id)
 VALUES ($1, $2, $3, $4, $5, $6)
@@ -530,35 +492,6 @@ func (q *Queries) InsertExecution(ctx context.Context, arg InsertExecutionParams
 	return err
 }
 
-const insertFeedback = `-- name: InsertFeedback :exec
-INSERT INTO feedback (entity_id, execution_id, outcome, observation, lesson,
-    unexpected_side_effects, tags)
-VALUES ($1, $2, $3, $4, $5, $6, $7)
-`
-
-type InsertFeedbackParams struct {
-	EntityID              uuid.UUID
-	ExecutionID           uuid.UUID
-	Outcome               string
-	Observation           *string
-	Lesson                *string
-	UnexpectedSideEffects []string
-	Tags                  []string
-}
-
-func (q *Queries) InsertFeedback(ctx context.Context, arg InsertFeedbackParams) error {
-	_, err := q.db.Exec(ctx, insertFeedback,
-		arg.EntityID,
-		arg.ExecutionID,
-		arg.Outcome,
-		arg.Observation,
-		arg.Lesson,
-		arg.UnexpectedSideEffects,
-		arg.Tags,
-	)
-	return err
-}
-
 const insertMetricSample = `-- name: InsertMetricSample :exec
 INSERT INTO metric_samples (entity_id, metric, value, tags, ts)
 VALUES ($1, $2, $3, $4, now())
@@ -581,41 +514,6 @@ func (q *Queries) InsertMetricSample(ctx context.Context, arg InsertMetricSample
 	return err
 }
 
-const insertSkill = `-- name: InsertSkill :exec
-INSERT INTO skills (entity_id, version, name, procedure, applies_type, action,
-    pattern_ids, status, changed_by, change_reason)
-VALUES ($1, $2, $3, $4, $5, $6, $7, $8, $9, $10)
-`
-
-type InsertSkillParams struct {
-	EntityID     uuid.UUID
-	Version      int32
-	Name         string
-	Procedure    []byte
-	AppliesType  *string
-	Action       string
-	PatternIds   []uuid.UUID
-	Status       string
-	ChangedBy    *uuid.UUID
-	ChangeReason *string
-}
-
-func (q *Queries) InsertSkill(ctx context.Context, arg InsertSkillParams) error {
-	_, err := q.db.Exec(ctx, insertSkill,
-		arg.EntityID,
-		arg.Version,
-		arg.Name,
-		arg.Procedure,
-		arg.AppliesType,
-		arg.Action,
-		arg.PatternIds,
-		arg.Status,
-		arg.ChangedBy,
-		arg.ChangeReason,
-	)
-	return err
-}
-
 const listApprovalRules = `-- name: ListApprovalRules :many
 SELECT id, entity_type, action, risk_class, autonomy_level, scope_entity, version, updated_at FROM approval_rules ORDER BY entity_type, action
 `
@@ -800,7 +698,11 @@ SELECT cd.entity_id, cd.target_id, cd.target_type, cd.kind, cd.config,
        e.slug AS entity_slug
 FROM check_defs cd
 JOIN entities e ON e.id = cd.entity_id
+LEFT JOIN entities tgt ON tgt.id = cd.target_id
 WHERE cd.enabled = true
+  AND (tgt.id IS NULL OR tgt.state IS NULL OR tgt.state NOT IN ('deprecated', 'destroyed'))
+  AND (cd.last_run_at IS NULL
+       OR cd.last_run_at <= now() - make_interval(secs => cd.interval_s))
 `
 
 type ListEnabledCheckDefsRow struct {
@@ -820,6 +722,9 @@ type ListEnabledCheckDefsRow struct {
 // =====================================================================
 // Phase 3 queries
 // =====================================================================
+// Enabled AND due. interval_s used to be selected but never filtered on, so
+// every check ran on every 30s pass and the declared intervals meant nothing.
+// NULL last_run_at = never run = due now.
 func (q *Queries) ListEnabledCheckDefs(ctx context.Context) ([]ListEnabledCheckDefsRow, error) {
 	rows, err := q.db.Query(ctx, listEnabledCheckDefs)
 	if err != nil {
@@ -852,44 +757,6 @@ func (q *Queries) ListEnabledCheckDefs(ctx context.Context) ([]ListEnabledCheckD
 	return items, nil
 }
 
-const listEntityStatus = `-- name: ListEntityStatus :many
-SELECT e.slug, e.type, st.health, st.last_check_at
-FROM entity_status st JOIN entities e ON e.id = st.entity_id
-ORDER BY e.slug
-`
-
-type ListEntityStatusRow struct {
-	Slug        string
-	Type        string
-	Health      string
-	LastCheckAt *time.Time
-}
-
-func (q *Queries) ListEntityStatus(ctx context.Context) ([]ListEntityStatusRow, error) {
-	rows, err := q.db.Query(ctx, listEntityStatus)
-	if err != nil {
-		return nil, err
-	}
-	defer rows.Close()
-	var items []ListEntityStatusRow
-	for rows.Next() {
-		var i ListEntityStatusRow
-		if err := rows.Scan(
-			&i.Slug,
-			&i.Type,
-			&i.Health,
-			&i.LastCheckAt,
-		); err != nil {
-			return nil, err
-		}
-		items = append(items, i)
-	}
-	if err := rows.Err(); err != nil {
-		return nil, err
-	}
-	return items, nil
-}
-
 const listEvents = `-- name: ListEvents :many
 SELECT id, ts, type, entity_id, severity, source, data, correlation_id
 FROM events
@@ -1270,6 +1137,20 @@ func (q *Queries) ListSkills(ctx context.Context, status *string) ([]Skill, erro
 	return items, nil
 }
 
+const markCheckRun = `-- name: MarkCheckRun :exec
+UPDATE check_defs SET last_run_at = now(), last_health = $2 WHERE entity_id = $1
+`
+
+type MarkCheckRunParams struct {
+	EntityID   uuid.UUID
+	LastHealth *string
+}
+
+func (q *Queries) MarkCheckRun(ctx context.Context, arg MarkCheckRunParams) error {
+	_, err := q.db.Exec(ctx, markCheckRun, arg.EntityID, arg.LastHealth)
+	return err
+}
+
 const putIdempotentResponse = `-- name: PutIdempotentResponse :exec
 INSERT INTO idempotency_keys (actor, key, request_hash, response_code, response_body)
 VALUES ($1, $2, $3, $4, $5)
@@ -1462,20 +1343,6 @@ func (q *Queries) UpdatePatternStatus(ctx context.Context, arg UpdatePatternStat
 	return err
 }
 
-const updateSignalState = `-- name: UpdateSignalState :exec
-UPDATE signals SET state = $2, updated_at = now() WHERE entity_id = $1
-`
-
-type UpdateSignalStateParams struct {
-	EntityID uuid.UUID
-	State    string
-}
-
-func (q *Queries) UpdateSignalState(ctx context.Context, arg UpdateSignalStateParams) error {
-	_, err := q.db.Exec(ctx, updateSignalState, arg.EntityID, arg.State)
-	return err
-}
-
 const updateSkillStatus = `-- name: UpdateSkillStatus :exec
 UPDATE skills SET status = $2, last_used_at = now() WHERE entity_id = $1 AND version = $2
 `
@@ -1605,3 +1472,25 @@ func (q *Queries) UpsertSignal(ctx context.Context, arg UpsertSignalParams) (Sig
 	)
 	return i, err
 }
+
+const worstHealthForTarget = `-- name: WorstHealthForTarget :one
+SELECT COALESCE(
+  (SELECT last_health FROM check_defs
+   WHERE enabled AND target_id = $1 AND last_health IS NOT NULL
+   ORDER BY CASE last_health
+     WHEN 'down' THEN 0 WHEN 'degraded' THEN 1 WHEN 'stale' THEN 2
+     WHEN 'unknown' THEN 3 ELSE 4 END
+   LIMIT 1),
+  'unknown')::text AS health
+`
+
+// An entity is as healthy as its unhealthiest check. Checks that have not run
+// yet (last_health IS NULL) are ignored rather than counted as unknown, so a
+// newly added check does not drag a known-good entity down before it has
+// produced a verdict.
+func (q *Queries) WorstHealthForTarget(ctx context.Context, targetID *uuid.UUID) (string, error) {
+	row := q.db.QueryRow(ctx, worstHealthForTarget, targetID)
+	var health string
+	err := row.Scan(&health)
+	return health, err
+}

internal/db/sqlcgen/relationships.sql.go

@@ -139,27 +139,3 @@ func (q *Queries) ListGraphEdges(ctx context.Context, arg ListGraphEdgesParams)
 	}
 	return items, nil
 }
-
-const upsertCurrentRelationship = `-- name: UpsertCurrentRelationship :exec
-INSERT INTO relationships (source_id, target_id, type, attributes, valid_from, valid_to)
-VALUES ($1, $2, $3, $4, now(), NULL)
-ON CONFLICT (source_id, target_id, type) WHERE valid_to IS NULL
-DO UPDATE SET attributes = EXCLUDED.attributes
-`
-
-type UpsertCurrentRelationshipParams struct {
-	SourceID   uuid.UUID
-	TargetID   uuid.UUID
-	Type       string
-	Attributes []byte
-}
-
-func (q *Queries) UpsertCurrentRelationship(ctx context.Context, arg UpsertCurrentRelationshipParams) error {
-	_, err := q.db.Exec(ctx, upsertCurrentRelationship,
-		arg.SourceID,
-		arg.TargetID,
-		arg.Type,
-		arg.Attributes,
-	)
-	return err
-}

internal/db/typetree.go

@@ -19,7 +19,8 @@ func LoadTypeTree(ctx context.Context, tx pgx.Tx) (*ontology.TypeTree, error) {
 	}
 
 	rows, err := tx.Query(ctx,
-		`SELECT name, COALESCE(parent_type,''), is_abstract, COALESCE(lifecycle_id,'')
+		`SELECT name, COALESCE(parent_type,''), is_abstract, COALESCE(lifecycle_id,''),
+		        layer, monitoring_spec
 		 FROM entity_types`)
 	if err != nil {
 		return nil, fmt.Errorf("load entity_types: %w", err)
@@ -27,10 +28,16 @@ func LoadTypeTree(ctx context.Context, tx pgx.Tx) (*ontology.TypeTree, error) {
 	for rows.Next() {
 		var name string
 		var info ontology.TypeInfo
-		if err := rows.Scan(&name, &info.Parent, &info.IsAbstract, &info.LifecycleID); err != nil {
+		// NULL monitoring_spec means the type declared nothing; '[]' means it
+		// declared "explicitly unmonitorable". Scanning through a pointer is
+		// what keeps those two apart — see ontology.TypeTree.Monitoring.
+		var monitoring *[]string
+		if err := rows.Scan(&name, &info.Parent, &info.IsAbstract, &info.LifecycleID,
+			&info.Layer, &monitoring); err != nil {
 			rows.Close()
 			return nil, err
 		}
+		info.Monitoring = monitoring
 		t.Types[name] = info
 	}
 	rows.Close()

internal/domain/domain_test.go

@@ -0,0 +1,139 @@
+package domain
+
+import (
+	"errors"
+	"testing"
+)
+
+func TestIsNil(t *testing.T) {
+	cases := []struct {
+		name string
+		u    UUID
+		want bool
+	}{
+		{"empty string", UUID(""), true},
+		{"single char", UUID("x"), false},
+		{"uuid string", UUID("550e8400-e29b-41d4-a716-446655440000"), false},
+		{"nil literal", UUID(""), true},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			got := c.u.IsNil()
+			if got != c.want {
+				t.Errorf("UUID(%q).IsNil() = %v, want %v", c.u, got, c.want)
+			}
+		})
+	}
+}
+
+func TestCanTransition(t *testing.T) {
+	type tc struct {
+		name string
+		from string
+		to   string
+		want bool
+	}
+	var cases []tc
+
+	for from, targets := range ValidSignalTransitions {
+		for _, to := range targets {
+			cases = append(cases, tc{from + "->" + to, from, to, true})
+		}
+	}
+
+	disallowed := []tc{
+		{"raised->raised", SignalRaised, SignalRaised, false},
+		{"resolved->raised", SignalResolved, SignalRaised, false},
+		{"failed->raised", SignalFailed, SignalRaised, false},
+		{"acknowledged->raised", SignalAcknowledged, SignalRaised, false},
+		{"muted->resolved", SignalMuted, SignalResolved, false},
+		{"acting->acknowledged", SignalActing, SignalAcknowledged, false},
+	}
+	cases = append(cases, disallowed...)
+
+	cases = append(cases,
+		tc{"unknown source", "nonexistent", SignalRaised, false},
+		tc{"unknown target", SignalRaised, "nonexistent", false},
+	)
+
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			s := &Signal{State: c.from}
+			got := s.CanTransition(c.to)
+			if got != c.want {
+				t.Errorf("CanTransition(%q -> %q) = %v, want %v", c.from, c.to, got, c.want)
+			}
+		})
+	}
+}
+
+func TestSentinelErrors(t *testing.T) {
+	cases := []struct {
+		name string
+		err  error
+		msg  string
+	}{
+		{"ErrNotFound", ErrNotFound, "entity not found"},
+		{"ErrInvalidTransition", ErrInvalidTransition, "invalid lifecycle transition"},
+		{"ErrApprovalRequired", ErrApprovalRequired, "operator approval required"},
+		{"ErrAutonomyBlocked", ErrAutonomyBlocked, "autonomy policy blocks this action"},
+		{"ErrConflict", ErrConflict, "concurrent modification conflict"},
+		{"ErrCircuitOpen", ErrCircuitOpen, "circuit breaker open for target"},
+		{"ErrAbstractType", ErrAbstractType, "cannot instantiate abstract entity type"},
+		{"ErrInvalidEdge", ErrInvalidEdge, "relationship endpoint type mismatch"},
+		{"ErrCardinality", ErrCardinality, "relationship cardinality violation"},
+		{"ErrSeedHashMismatch", ErrSeedHashMismatch, "seed content hash mismatch"},
+		{"ErrAlreadyExists", ErrAlreadyExists, "entity already exists"},
+		{"ErrQuarantined", ErrQuarantined, "pattern is quarantined"},
+		{"ErrSkillDeprecated", ErrSkillDeprecated, "skill is deprecated"},
+		{"ErrInvalidInput", ErrInvalidInput, "invalid input"},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			if c.err == nil {
+				t.Fatal("sentinel error is nil")
+			}
+			if !errors.Is(c.err, c.err) {
+				t.Errorf("errors.Is failed for %s", c.name)
+			}
+			if c.err.Error() != c.msg {
+				t.Errorf("Error() = %q, want %q", c.err.Error(), c.msg)
+			}
+		})
+	}
+}
+
+func TestSignalTransitionsComplete(t *testing.T) {
+	// Non-terminal states must be keys in ValidSignalTransitions.
+	// SignalResolved is a terminal state (no outgoing transitions) and is
+	// intentionally absent from the map.
+	nonTerminal := []string{
+		SignalRaised,
+		SignalAcknowledged,
+		SignalActing,
+		SignalMuted,
+		SignalFailed,
+	}
+	for _, state := range nonTerminal {
+		targets, ok := ValidSignalTransitions[state]
+		if !ok {
+			t.Errorf("non-terminal state %q missing from ValidSignalTransitions", state)
+			continue
+		}
+		if len(targets) == 0 {
+			t.Errorf("state %q maps to empty transition list", state)
+		}
+	}
+
+	// Resolved is terminal: it should not appear as a source key.
+	if _, ok := ValidSignalTransitions[SignalResolved]; ok {
+		t.Errorf("terminal state %q should not have outgoing transitions", SignalResolved)
+	}
+
+	// No state anywhere in the map may map to nil/empty.
+	for state, targets := range ValidSignalTransitions {
+		if len(targets) == 0 {
+			t.Errorf("state %q maps to empty/nil transition list", state)
+		}
+	}
+}

internal/execlog/execlog.go

@@ -0,0 +1,135 @@
+// Package execlog persists incremental command output for an execution and
+// announces it on the event stream.
+//
+// It exists as its own package because both SSH execution paths need it —
+// internal/mcp (the agent's auto-run windows) and internal/httpapi (the
+// post-approval actuator). Those two already carry near-identical copies of
+// sshExec, and every bug found in this area so far has been a case of the two
+// copies drifting apart; one shared sink is the cheap way not to repeat that.
+package execlog
+
+import (
+	"context"
+	"log/slog"
+	"sync"
+	"time"
+
+	"github.com/dtoro/oikos/internal/db"
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+)
+
+// eventInterval throttles execution.output events. Chunks are persisted as
+// they arrive, but a chatty command (apt, a long build) can produce hundreds
+// per second and the SSE broker drops events for slow subscribers — flooding
+// it would push out the signal.* and approval.* events that actually need to
+// arrive. The event is only a "there is more output" ping; subscribers re-read
+// the rows.
+const eventInterval = time.Second
+
+// Sink receives output chunks as they arrive from a remote command.
+type Sink func(stream string, chunk []byte)
+
+// New returns a Sink that writes chunks to execution_logs and emits a
+// throttled execution.output event, plus a Flush to call when the command
+// finishes.
+//
+// The returned Sink is safe for concurrent use: stdout and stderr are written
+// from separate goroutines.
+func New(ctx context.Context, pool *db.Pool, execID uuid.UUID, correlationID string) (Sink, func()) {
+	var (
+		mu        sync.Mutex
+		seq       int
+		lastEvent time.Time
+		pending   bool
+	)
+
+	emit := func() {
+		if err := observability.Event(ctx, sqlcgen.New(pool), "execution.output", &execID,
+			"info", "actuator", correlationID, map[string]any{"execution_id": execID.String()}); err != nil {
+			slog.Debug("execlog: emit output event", "error", err, "execution_id", execID)
+		}
+	}
+
+	sink := func(stream string, chunk []byte) {
+		if len(chunk) == 0 {
+			return
+		}
+		mu.Lock()
+		seq++
+		n := seq
+		mu.Unlock()
+
+		// A failed log write must never fail the command: this is observability,
+		// and the authoritative output still lands in executions.result at the
+		// end. Log and carry on.
+		if _, err := pool.Exec(ctx,
+			`INSERT INTO execution_logs (execution_id, seq, stream, chunk)
+			 VALUES ($1, $2, $3, $4)`,
+			execID, n, stream, string(chunk)); err != nil {
+			slog.Debug("execlog: persist chunk", "error", err, "execution_id", execID)
+			return
+		}
+
+		mu.Lock()
+		due := time.Since(lastEvent) >= eventInterval
+		if due {
+			lastEvent = time.Now()
+			pending = false
+		} else {
+			pending = true
+		}
+		mu.Unlock()
+
+		if due {
+			emit()
+		}
+	}
+
+	// Flush emits a final event when output arrived inside the throttle window,
+	// so the last few lines of a short command are not left unannounced.
+	flush := func() {
+		mu.Lock()
+		due := pending
+		pending = false
+		mu.Unlock()
+		if due {
+			emit()
+		}
+	}
+
+	return sink, flush
+}
+
+// Read returns an execution's persisted output in order.
+func Read(ctx context.Context, pool *db.Pool, execID uuid.UUID, limit int) ([]Chunk, error) {
+	if limit <= 0 {
+		limit = 1000
+	}
+	rows, err := pool.Query(ctx,
+		`SELECT seq, stream, chunk, ts FROM execution_logs
+		 WHERE execution_id = $1 ORDER BY seq LIMIT $2`, execID, limit)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	var out []Chunk
+	for rows.Next() {
+		var c Chunk
+		if err := rows.Scan(&c.Seq, &c.Stream, &c.Chunk, &c.TS); err != nil {
+			return nil, err
+		}
+		out = append(out, c)
+	}
+	return out, rows.Err()
+}
+
+// Chunk is one persisted slice of command output.
+type Chunk struct {
+	Seq    int       `json:"seq"`
+	Stream string    `json:"stream"`
+	Chunk  string    `json:"chunk"`
+	TS     time.Time `json:"ts"`
+}

internal/httpapi/actuator.go

@@ -0,0 +1,751 @@
+package httpapi
+
+import (
+	"bytes"
+	"context"
+	"encoding/base64"
+	"encoding/json"
+	"fmt"
+	"log/slog"
+	"os"
+	"strconv"
+	"strings"
+	"sync"
+	"time"
+
+	"github.com/dtoro/oikos/internal/db"
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/execlog"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+	"golang.org/x/crypto/ssh"
+)
+
+var (
+	_sshUser string
+	_sshKey  []byte
+)
+
+// flexBool accepts a JSON bool, number (0/1), or string ("true"/"1"/"yes").
+// LLMs routinely emit `"privileged": 0` instead of `false`; a strict `bool`
+// field made the approved pct_create execution fail to parse *after* the
+// operator had already approved it — the container was never created and the
+// operator saw "queued" with no result. This type tolerates the common shapes.
+type flexBool bool
+
+func (b *flexBool) UnmarshalJSON(data []byte) error {
+	s := strings.TrimSpace(strings.Trim(string(data), `"`))
+	switch strings.ToLower(s) {
+	case "true", "1", "yes", "on":
+		*b = true
+	case "false", "0", "no", "off", "", "null":
+		*b = false
+	default:
+		return fmt.Errorf("cannot parse %q as bool", s)
+	}
+	return nil
+}
+
+func initSSH() {
+	if _sshUser == "" {
+		_sshUser = os.Getenv("OIKOS_SSH_USER")
+		if _sshUser == "" {
+			_sshUser = "root"
+		}
+	}
+	if len(_sshKey) == 0 {
+		keyPath := os.Getenv("OIKOS_SSH_KEY_PATH")
+		if keyPath == "" {
+			keyPath = "/etc/oikos/ssh_key"
+		}
+		var err error
+		_sshKey, err = os.ReadFile(keyPath)
+		if err != nil {
+			slog.Warn("httpapi ssh: cannot read key", "path", keyPath, "error", err)
+		}
+	}
+}
+
+// sshExecTimeout bounds how long a single remote command may run. Without
+// this, a hung remote command (e.g. a piped install script stuck retrying
+// DNS against a misconfigured gateway) blocks the executing goroutine
+// forever: the execution never leaves 'approved'/'running', the operator
+// sees an unkillable spinner, and get_execution_status has nothing new to
+// report. Generous enough for a real apt/docker install; not infinite.
+const sshExecTimeout = 10 * time.Minute
+
+// streamWriter buffers everything it is given while forwarding each write to a
+// sink. One on session.Stdout and another sharing the same buffer on
+// session.Stderr reproduces CombinedOutput's interleaving in the order the
+// remote end produced it. Mirrors the twin in internal/mcp/server.go.
+type streamWriter struct {
+	mu     *sync.Mutex
+	buf    *bytes.Buffer
+	stream string
+	sink   execlog.Sink
+}
+
+func (w *streamWriter) Write(p []byte) (int, error) {
+	w.mu.Lock()
+	w.buf.Write(p)
+	w.mu.Unlock()
+	if w.sink != nil {
+		// Copy: the ssh library reuses p once Write returns.
+		w.sink(w.stream, append([]byte(nil), p...))
+	}
+	return len(p), nil
+}
+
+func sshExec(ctx context.Context, host, user, command string) (string, error) {
+	return sshExecStream(ctx, host, user, command, nil)
+}
+
+// sshExecStream runs a command and reports its combined output, forwarding
+// each chunk to sink as it arrives. A nil sink behaves exactly as before.
+func sshExecStream(ctx context.Context, host, user, command string, sink execlog.Sink) (string, error) {
+	initSSH()
+	if len(_sshKey) == 0 {
+		return "", fmt.Errorf("no SSH key available")
+	}
+	if user == "" {
+		user = _sshUser
+	}
+
+	addr := host + ":22"
+	signer, err := ssh.ParsePrivateKey(_sshKey)
+	if err != nil {
+		return "", fmt.Errorf("parse key: %w", err)
+	}
+
+	cfg := &ssh.ClientConfig{
+		User:            user,
+		Auth:            []ssh.AuthMethod{ssh.PublicKeys(signer)},
+		HostKeyCallback: ssh.InsecureIgnoreHostKey(),
+		Timeout:         10 * time.Second,
+	}
+
+	client, err := ssh.Dial("tcp", addr, cfg)
+	if err != nil {
+		return "", fmt.Errorf("dial %s: %w", host, err)
+	}
+	defer client.Close()
+
+	session, err := client.NewSession()
+	if err != nil {
+		return "", fmt.Errorf("session: %w", err)
+	}
+	defer session.Close()
+
+	var (
+		mu  sync.Mutex
+		buf bytes.Buffer
+	)
+	session.Stdout = &streamWriter{mu: &mu, buf: &buf, stream: "stdout", sink: sink}
+	session.Stderr = &streamWriter{mu: &mu, buf: &buf, stream: "stderr", sink: sink}
+
+	collected := func() string {
+		mu.Lock()
+		defer mu.Unlock()
+		return strings.TrimSpace(buf.String())
+	}
+
+	done := make(chan error, 1)
+	go func() {
+		// See internal/mcp/server.go's sshExec for why this recovers rather
+		// than letting a rare SSH-library panic crash the whole api process.
+		defer func() {
+			if r := recover(); r != nil {
+				done <- fmt.Errorf("panic in ssh exec: %v", r)
+			}
+		}()
+		// Run rather than CombinedOutput so the assigned writers are used;
+		// Run returns only after both streams are fully drained.
+		done <- session.Run(command)
+	}()
+
+	select {
+	case err := <-done:
+		text := collected()
+		// A non-zero exit MUST surface as an error. The previous guard only
+		// errored when there was no output, so a `pct create` that printed
+		// "CT 132 already exists" and exited non-zero was reported as
+		// success — the execution was marked completed though nothing was
+		// provisioned.
+		if err != nil {
+			if text != "" {
+				return text, fmt.Errorf("%w: %s", err, text)
+			}
+			return text, fmt.Errorf("exec: %w", err)
+		}
+		return text, nil
+	case <-time.After(sshExecTimeout):
+		// Close the session/client to hang up the remote side; the
+		// goroutine above will eventually exit once that unblocks Run, but we
+		// don't wait for it — the caller needs an answer now, not an
+		// indefinite hang.
+		session.Close()
+		client.Close()
+		// Return what arrived before it hung, rather than "". A provisioning
+		// command that stalls halfway is precisely when its output matters.
+		return collected(), fmt.Errorf("timed out after %s waiting for command to finish on %s", sshExecTimeout, host)
+	case <-ctx.Done():
+		session.Close()
+		client.Close()
+		return collected(), ctx.Err()
+	}
+}
+
+func resolveHostSSH(ctx context.Context, pool *db.Pool, entitySlug string) (string, string, error) {
+	var attrs string
+	err := pool.QueryRow(ctx, "SELECT attributes::text FROM entities WHERE slug = $1", entitySlug).Scan(&attrs)
+	if err != nil {
+		return "", "", fmt.Errorf("entity not found: %s", entitySlug)
+	}
+
+	var m map[string]interface{}
+	if err := json.Unmarshal([]byte(attrs), &m); err != nil {
+		return "", "", fmt.Errorf("parse attributes: %w", err)
+	}
+
+	sshUser := _sshUser
+	if sshUser == "" {
+		sshUser = "root"
+	}
+
+	if ip, ok := m["lan_ip"].(string); ok && ip != "" {
+		return ip, sshUser, nil
+	}
+	if mesh, ok := m["mesh"].(map[string]interface{}); ok {
+		for _, proto := range []string{"netbird", "tailscale"} {
+			if p, ok := mesh[proto].(map[string]interface{}); ok {
+				if ip, ok := p["ip"].(string); ok && ip != "" {
+					return ip, sshUser, nil
+				}
+			}
+		}
+	}
+	return "", "", fmt.Errorf("no IP found for %s", entitySlug)
+}
+
+// resolveRunTarget mirrors internal/mcp.resolveExecTarget for the approved-
+// execution side: any target slug (host: or lxc:) resolves to the SSH
+// endpoint that runs the command plus a wrap function that turns a plain
+// shell command into what actually needs to be sent — identity for a host,
+// `pct exec <pve_id>` for an LXC. Kept as a small duplicate rather than a
+// cross-package import to avoid coupling httpapi to mcp for one helper.
+func resolveRunTarget(ctx context.Context, pool *db.Pool, targetSlug string) (host, user string, wrap func(string) string, err error) {
+	if strings.HasPrefix(targetSlug, "host:") {
+		host, user, err = resolveHostSSH(ctx, pool, targetSlug)
+		return host, user, func(cmd string) string { return cmd }, err
+	}
+	if strings.HasPrefix(targetSlug, "lxc:") {
+		var pveID, hostAttr string
+		// COALESCE the host column: many older LXC entities (seeded from
+		// inventory, not provisioned by pct_create) have pve_id but no host
+		// attribute at all. Scanning a SQL NULL into a plain string errors
+		// the whole row, wrongly reporting "missing pve_id" even when it was
+		// present — COALESCE avoids the NULL, "" is handled below.
+		if qerr := pool.QueryRow(ctx, "SELECT attributes->>'pve_id', COALESCE(attributes->>'host', '') FROM entities WHERE slug = $1", targetSlug).Scan(&pveID, &hostAttr); qerr != nil || pveID == "" {
+			return "", "", nil, fmt.Errorf("LXC not found or missing pve_id: %s", targetSlug)
+		}
+		hostSlug := hostAttr
+		if hostSlug == "" {
+			hostSlug = "hubris"
+		}
+		if !strings.HasPrefix(hostSlug, "host:") {
+			hostSlug = "host:" + hostSlug
+		}
+		host, user, err = resolveHostSSH(ctx, pool, hostSlug)
+		id := pveID
+		return host, user, func(cmd string) string {
+			b64 := base64.StdEncoding.EncodeToString([]byte(cmd))
+			return fmt.Sprintf("pct exec %s -- bash -c 'echo %s | base64 -d | bash'", id, b64)
+		}, err
+	}
+	return "", "", nil, fmt.Errorf("unsupported target %q: must be host:<slug> or lxc:<slug>", targetSlug)
+}
+
+// executeApprovedAction runs a gated action after operator approval.
+// Runs in a background goroutine to not block the HTTP response.
+// emitExecutionEvent records an execution lifecycle event for SSE fan-out so
+// the control room can watch approved actions run to completion live.
+func emitExecutionEvent(ctx context.Context, pool *db.Pool, execID uuid.UUID, status string, detail map[string]any) {
+	severity := "info"
+	if status == "failed" {
+		severity = "warning"
+	}
+	// The correlation id was hardcoded to "", so execution events could not be
+	// tied back to the session that caused them — the one join you want when
+	// asking "what did this agent turn actually do?". It is already on the
+	// execution row; read it rather than threading it through eleven callers.
+	var correlationID string
+	if err := pool.QueryRow(ctx,
+		`SELECT correlation_id FROM executions WHERE entity_id = $1`, execID).Scan(&correlationID); err != nil {
+		correlationID = ""
+	}
+	_ = observability.Event(ctx, sqlcgen.New(pool), "execution."+status, &execID, severity, "actuator", correlationID, detail)
+	if status == "completed" || status == "failed" || status == "cancelled" {
+		closePlanStepForExecution(ctx, pool, execID, status)
+	}
+}
+
+// closePlanStepForExecution auto-closes a task plan step whose linked execution
+// just reached a terminal state, so the task board advances even if the agent
+// doesn't call update_plan_step itself (belt and suspenders — the agent links
+// the step to the execution when it starts it; the api finishes it here). Emits
+// plan.step.finished correlated to the step's session. No-op for the vast
+// majority of executions, which aren't plan steps.
+func closePlanStepForExecution(ctx context.Context, pool *db.Pool, execID uuid.UUID, execStatus string) {
+	stepStatus := "done"
+	if execStatus == "failed" || execStatus == "cancelled" {
+		stepStatus = "failed"
+	}
+	var stepID, sessionID string
+	var seq int
+	if err := pool.QueryRow(ctx, `
+		UPDATE session_plan_steps SET status = $2, finished_at = now()
+		WHERE execution_id = $1 AND status NOT IN ('done', 'failed', 'skipped')
+		RETURNING id::text, session_id::text, seq`, execID, stepStatus).Scan(&stepID, &sessionID, &seq); err != nil {
+		return // no matching open step
+	}
+	_ = observability.Event(ctx, sqlcgen.New(pool), "plan.step.finished", &execID, "info", "actuator", sessionID,
+		map[string]any{"step_id": stepID, "seq": seq, "status": stepStatus, "execution_id": execID.String()})
+}
+
+func executeApprovedAction(ctx context.Context, pool *db.Pool, execID uuid.UUID, targetSlug string, actionStr string) {
+	slog.Info("httpapi: executing approved action", "execution_id", execID, "target", targetSlug, "action", actionStr)
+
+	host, user, wrap, err := resolveRunTarget(ctx, pool, targetSlug)
+	if err != nil {
+		slog.Error("httpapi: resolve host for approved execution", "error", err, "target", targetSlug)
+		pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+			execID, jsonErr("%s", err.Error()))
+		emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": err.Error()})
+		return
+	}
+
+	idx := strings.Index(actionStr, ":")
+	if idx < 0 {
+		slog.Error("httpapi: malformed action string (no colon)", "action", actionStr)
+		return
+	}
+	action, params := actionStr[:idx], actionStr[idx+1:]
+
+	startedAt := time.Now()
+	// Persist started_at now, not at the end. It was captured here but only
+	// written in the terminal UPDATE, so a running execution reported
+	// started_at = NULL for its entire life — the UI could not show how long
+	// anything had been going, which is exactly when you want to know.
+	if _, err := pool.Exec(ctx,
+		`UPDATE executions SET status = 'running', started_at = $2 WHERE entity_id = $1`,
+		execID, startedAt); err != nil {
+		slog.Error("httpapi: mark execution running", "error", err, "execution_id", execID)
+	}
+
+	// Stream output for the actions whose output an operator actually watches:
+	// a long apt upgrade, a pct create, an arbitrary approved `run`. The small
+	// internal lookups further down (listing template cache, pvesh nextid) stay
+	// unstreamed — they are plumbing, and logging them would bury the command
+	// the operator approved.
+	var correlationID string
+	if qerr := pool.QueryRow(ctx,
+		`SELECT correlation_id FROM executions WHERE entity_id = $1`, execID).Scan(&correlationID); qerr != nil {
+		correlationID = ""
+	}
+	sink, flushLogs := execlog.New(ctx, pool, execID, correlationID)
+	defer flushLogs()
+
+	var output, cmd string
+
+	switch action {
+	case "systemctl":
+		svc := strings.TrimPrefix(targetSlug, "lxc:")
+		switch {
+		case strings.HasPrefix(params, "enable:"):
+			svc = strings.TrimPrefix(params, "enable:")
+			cmd = fmt.Sprintf("systemctl enable %s --now 2>&1; sleep 1; systemctl is-active %s", svc, svc)
+		case strings.HasPrefix(params, "disable:"):
+			svc = strings.TrimPrefix(params, "disable:")
+			cmd = fmt.Sprintf("systemctl disable %s --now 2>&1; sleep 1; systemctl is-active %s", svc, svc)
+		default:
+			cmd = fmt.Sprintf("systemctl %s %s 2>&1", params, svc)
+		}
+		output, err = sshExecStream(ctx, host, user, cmd, sink)
+
+	case "apt_upgrade":
+		svc := strings.TrimPrefix(targetSlug, "lxc:")
+		cmd = fmt.Sprintf("apt update -qq 2>&1 >/dev/null && apt upgrade -y -qq 2>&1; echo '---'; systemctl is-active %s || true", svc)
+		output, err = sshExecStream(ctx, host, user, cmd, sink)
+
+	case "pct_create":
+		var cfg struct {
+			VMID         int      `json:"vmid"`
+			Hostname     string   `json:"hostname"`
+			Cores        int      `json:"cores"`
+			Memory       int      `json:"memory"`
+			DiskGB       int      `json:"disk_gb"`
+			IP           string   `json:"ip"`
+			GW           string   `json:"gw"`
+			Bridge       string   `json:"bridge"` // e.g. vmbr0/vmbr1 — which bridge actually reaches the target subnet on this host varies per host, don't assume vmbr0
+			Storage      string   `json:"storage"`
+			Template     string   `json:"template"`
+			Privileged   flexBool `json:"privileged"`
+			Nesting      flexBool `json:"nesting"`
+			Mounts       []string `json:"mounts"`
+			Nameserver   string   `json:"nameserver"`
+			Searchdomain string   `json:"searchdomain"`
+			// No services/post_install here anymore — pct_create is atomic
+			// (create + start + register only). Installing packages and
+			// running setup scripts is the agent's job via follow-up `run`
+			// calls against lxc:<hostname>, so each step is individually
+			// observable and recoverable instead of one opaque multi-minute
+			// black box. See the comment above the removed post-create block.
+		}
+		if err := json.Unmarshal([]byte(params), &cfg); err != nil {
+			slog.Error("httpapi: pct_create parse params", "error", err, "params", params)
+			pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+				execID, jsonErr("invalid pct_create params: %v", err))
+			emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": err.Error()})
+			return
+		}
+		// Only hostname is required. vmid is optional — when 0 (or later found
+		// to collide) the VMID guard below assigns a free cluster id.
+		if cfg.Hostname == "" {
+			pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+				execID, `{"error":"pct_create: hostname is required"}`)
+			emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": "missing hostname"})
+			return
+		}
+		if cfg.Cores == 0 {
+			cfg.Cores = 1
+		}
+		if cfg.Memory == 0 {
+			cfg.Memory = 512
+		}
+		if cfg.DiskGB == 0 {
+			cfg.DiskGB = 8
+		}
+		if cfg.Storage == "" {
+			cfg.Storage = "local-lvm"
+		}
+		if cfg.GW == "" {
+			cfg.GW = "192.168.8.2"
+		}
+		if cfg.Nameserver == "" {
+			cfg.Nameserver = "192.168.8.2"
+		}
+		if cfg.Searchdomain == "" {
+			cfg.Searchdomain = "hubris.network"
+		}
+		// Template pre-flight: resolve against what the host actually has
+		// cached. A hardcoded name (e.g. debian-13) fails opaquely with a raw
+		// `pct` error when that exact file isn't present. List the cache, then
+		// either validate the requested template or auto-pick the newest
+		// debian one; on miss, fail early with the available list so the
+		// operator/agent can retry with a real name.
+		cacheList, tplErr := sshExec(ctx, host, user, "ls -1 /var/lib/vz/template/cache/ 2>/dev/null | grep -E '\\.tar\\.(zst|gz|xz)$' || true")
+		available := []string{}
+		for _, l := range strings.Split(strings.TrimSpace(cacheList), "\n") {
+			if l = strings.TrimSpace(l); l != "" {
+				available = append(available, l)
+			}
+		}
+		if tplErr != nil {
+			pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+				execID, jsonErr("list templates on %s: %s", targetSlug, tplErr.Error()))
+			emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": tplErr.Error()})
+			return
+		}
+		cfg.Template = resolveTemplate(cfg.Template, available)
+		if cfg.Template == "" {
+			msg := fmt.Sprintf("no usable LXC template on %s. Available: %v", targetSlug, available)
+			pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+				execID, jsonErr("%s", msg))
+			emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": msg})
+			return
+		}
+
+		// VMID collision guard. Proxmox VMIDs are cluster-wide, so the model's
+		// guess (e.g. 132) can collide with a container on another node — pct
+		// create then fails with "CT N already exists on node X". Fetch the set
+		// of in-use VMIDs across the cluster; if the requested id is taken (or
+		// absent), fall back to the cluster's next free id so provisioning
+		// still succeeds instead of dead-ending on the operator's approval.
+		usedRaw, _ := sshExec(ctx, host, user, `pvesh get /cluster/resources --type vm --output-format json 2>/dev/null | grep -o '"vmid":[0-9]*' | grep -o '[0-9]*' || true`)
+		used := map[int]bool{}
+		for _, l := range strings.Fields(usedRaw) {
+			if n, e := strconv.Atoi(strings.TrimSpace(l)); e == nil {
+				used[n] = true
+			}
+		}
+		if cfg.VMID == 0 || used[cfg.VMID] {
+			nextRaw, nerr := sshExec(ctx, host, user, `pvesh get /cluster/nextid 2>/dev/null`)
+			nextID, cerr := strconv.Atoi(strings.TrimSpace(nextRaw))
+			if nerr != nil || cerr != nil || nextID == 0 {
+				msg := fmt.Sprintf("VMID %d is already in use on the cluster and could not resolve a free id", cfg.VMID)
+				pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+					execID, jsonErr("%s", msg))
+				emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": msg})
+				return
+			}
+			slog.Info("httpapi: pct_create VMID reassigned", "requested", cfg.VMID, "assigned", nextID)
+			cfg.VMID = nextID
+		}
+
+		privFlag := "--unprivileged 1"
+		if cfg.Privileged {
+			privFlag = "--unprivileged 0"
+		}
+
+		nestingFlag := ""
+		features := []string{}
+		if cfg.Nesting {
+			features = append(features, "nesting=1")
+		}
+		if cfg.Privileged {
+			features = append(features, "keyctl=1")
+		}
+		if len(features) > 0 {
+			nestingFlag = fmt.Sprintf(" --features %s", strings.Join(features, ","))
+		}
+
+		if cfg.Bridge == "" {
+			cfg.Bridge = "vmbr0"
+		}
+
+		// net0: DHCP when no static IP is given (or ip=="dhcp"). Proxmox
+		// rejects a gateway alongside ip=dhcp, so only add gw for a static IP.
+		net0 := "name=eth0,bridge=" + cfg.Bridge + ","
+		isStatic := cfg.IP != "" && !strings.EqualFold(cfg.IP, "dhcp")
+		if !isStatic {
+			net0 += "ip=dhcp"
+		} else {
+			net0 += "ip=" + cfg.IP
+			if cfg.GW != "" {
+				net0 += ",gw=" + cfg.GW
+			}
+		}
+
+		// Pre-flight: for a static config, ping the gateway from the target
+		// HOST, on the SPECIFIC BRIDGE being requested, before spending 5+
+		// minutes creating the container. This is the check that would have
+		// caught the real TypeType failure immediately instead of after a
+		// full provision attempt.
+		//
+		// Binding to the bridge (`ping -I <bridge>`) matters and was found
+		// live: a plain unqualified `ping <gw>` from the host can succeed via
+		// the host's own routing table (multiple routes, possibly through an
+		// upstream router) even when the *container* — which only gets a
+		// naive on-link default route via its bridge's veth — can never ARP
+		// that gateway at all. Confirmed on `strong`: bare `ping 192.168.8.2`
+		// succeeded (via the host's default route), but a container actually
+		// attached to vmbr0 showed 100% packet loss trying to reach the same
+		// address, because vmbr0 doesn't carry that subnet's L2 segment.
+		// Binding to the bridge interface reproduces what the container will
+		// actually experience, not what the host's broader routing table can
+		// reach.
+		if isStatic && cfg.GW != "" {
+			pingOut, pingErr := sshExec(ctx, host, user, fmt.Sprintf("ping -I %s -c1 -W2 %s >/dev/null 2>&1 && echo PREFLIGHT_OK || echo PREFLIGHT_FAIL", cfg.Bridge, cfg.GW))
+			if pingErr != nil || !gatewayPreflightPassed(pingOut) {
+				msg := fmt.Sprintf(
+					"gateway %s is not reachable from %s on bridge %s — this almost always means the bridge doesn't carry that subnet on this host (each bridge only reaches the network it's physically wired to). "+
+						"Do not retry with a different gateway guess in the same subnet: find an existing LXC on this host with an IP in the same /28 and copy its exact bridge+gateway, or use DHCP instead.",
+					cfg.GW, targetSlug, cfg.Bridge)
+				pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+					execID, jsonErr("%s", msg))
+				emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": msg})
+				return
+			}
+		}
+
+		templatePath := fmt.Sprintf("/var/lib/vz/template/cache/%s", cfg.Template)
+		createCmd := fmt.Sprintf(
+			"pct create %d %s --hostname %s --cores %d --memory %d --rootfs %s:%d %s --net0 %s%s --start 1",
+			cfg.VMID, templatePath, cfg.Hostname, cfg.Cores, cfg.Memory,
+			cfg.Storage, cfg.DiskGB, privFlag, net0, nestingFlag)
+
+		if cfg.Nameserver != "" {
+			createCmd += fmt.Sprintf(" --nameserver %s", cfg.Nameserver)
+		}
+		if cfg.Searchdomain != "" {
+			createCmd += fmt.Sprintf(" --searchdomain %s", cfg.Searchdomain)
+		}
+
+		// Add mount points
+		for i, mp := range cfg.Mounts {
+			if i < 10 { // pct supports up to mp9
+				createCmd += fmt.Sprintf(" --mp%d %s", i, mp)
+			}
+		}
+
+		slog.Info("httpapi: pct_create running", "vmid", cfg.VMID, "hostname", cfg.Hostname, "cmd", createCmd)
+		output, err = sshExecStream(ctx, host, user, createCmd, sink)
+
+		// pct_create is now DELIBERATELY ATOMIC: create + start + register,
+		// nothing else. It used to also run apt installs and a post_install
+		// script inline as one black-box multi-minute SSH call — the agent
+		// got back a single opaque success/fail for the whole thing with no
+		// way to see (or fix) which step actually broke. That's the opposite
+		// of what makes an agent able to recover from errors.
+		//
+		// Installing packages, running post_install, and verifying the
+		// service now happen as the agent's OWN follow-up `run` calls against
+		// the new lxc:<hostname> target — each one is synchronous (in an
+		// active assent window) or individually gated, so the agent observes
+		// every step's real output and can diagnose + retry the exact thing
+		// that failed instead of re-doing the whole container. See SOUL.md
+		// "After pct_create: you drive the install" and provisionScript's
+		// surviving role (DNS self-heal) is now something the agent invokes
+		// itself via `run`, not something baked into this handler.
+		//
+		// cfg.Services/cfg.PostInstall are intentionally no longer read here.
+
+		// On success, register the entity in the DB with proper relationships
+		if err == nil {
+			slug := "lxc:" + cfg.Hostname
+			var lxcID uuid.UUID
+			lxcID, _ = uuid.NewV7()
+			attrs := map[string]any{
+				"pve_id": fmt.Sprintf("%d", cfg.VMID),
+				"host":   strings.TrimPrefix(targetSlug, "host:"),
+				"ip":     cfg.IP,
+			}
+			attrsJSON, _ := json.Marshal(attrs)
+			_, insErr := pool.Exec(ctx, `INSERT INTO entities (id, slug, type, name, state, attributes, enrolled_at)
+				VALUES ($1, $2, 'lxc', $3, 'provisioning', $4, now()) ON CONFLICT (slug) DO NOTHING`, lxcID, slug, cfg.Hostname, attrsJSON)
+			if insErr != nil {
+				slog.Error("httpapi: pct_create entity insert", "error", insErr, "slug", slug)
+			}
+
+			// Create hosts relationship: Proxmox host → LXC
+			var hostID uuid.UUID
+			if err := pool.QueryRow(ctx, "SELECT id FROM entities WHERE slug = $1", targetSlug).Scan(&hostID); err == nil {
+				_, relErr := pool.Exec(ctx, `INSERT INTO relationships (source_id, target_id, type, attributes, valid_from)
+					VALUES ($1, $2, 'hosts', '{"provisioned_by":"nomos"}'::jsonb, now())`, hostID, lxcID)
+				if relErr != nil {
+					slog.Error("httpapi: pct_create relationship insert", "error", relErr, "host", targetSlug, "lxc", slug)
+				}
+			}
+
+			// Create entity_status row for health tracking
+			pool.Exec(ctx, `INSERT INTO entity_status (entity_id, health, last_check_at)
+				VALUES ($1, 'unknown', now()) ON CONFLICT (entity_id) DO NOTHING`, lxcID)
+
+			emitExecutionEvent(ctx, pool, execID, "executing", map[string]any{
+				"lxc_slug": slug, "vmid": cfg.VMID, "host": targetSlug,
+			})
+
+			slog.Info("httpapi: pct_create entity registered", "slug", slug, "vmid", cfg.VMID, "host", targetSlug)
+		}
+
+	case "run":
+		// The general gated primitive: arbitrary shell against any host or
+		// LXC, approved and classified by internal/policy.ClassifyCommand at
+		// request time (see mcp/server.go's "run" tool). No fixed action
+		// enum — new capability doesn't require new Go code here.
+		var cfg struct {
+			Command string `json:"command"`
+			Purpose string `json:"purpose"`
+		}
+		if perr := json.Unmarshal([]byte(params), &cfg); perr != nil {
+			pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+				execID, jsonErr("invalid run params: %v", perr))
+			emitExecutionEvent(ctx, pool, execID, "failed", map[string]any{"target": targetSlug, "error": perr.Error()})
+			return
+		}
+		cmd = wrap(cfg.Command)
+		output, err = sshExecStream(ctx, host, user, cmd, sink)
+
+	default:
+		slog.Error("httpapi: unknown gated action for approved execution", "action", action, "execution_id", execID)
+		pool.Exec(ctx, `UPDATE executions SET status='failed', result=$2::jsonb WHERE entity_id=$1`,
+			execID, jsonErr("unknown action: %s", action))
+		return
+	}
+
+	durationMs := int(time.Since(startedAt).Milliseconds())
+	status := "completed"
+	verified := true
+	// Build result via json.Marshal, not string interpolation. Command output
+	// (apt/pct) contains quotes, backslashes and control chars; the old
+	// fmt.Sprintf only escaped "\n", producing invalid JSON that failed the
+	// ::jsonb cast — so this UPDATE was silently discarded and the execution
+	// was stuck at "approved" forever even though provisioning succeeded.
+	resMap := map[string]any{"output": output}
+	if err != nil {
+		resMap["error"] = err.Error()
+		status = "failed"
+		verified = false
+	}
+	resultJSON, _ := json.Marshal(resMap)
+
+	if _, uerr := pool.Exec(ctx, `UPDATE executions SET status=$2, result=$3::jsonb, duration_ms=$4, verified=$5, started_at=$6, completed_at=$7 WHERE entity_id=$1`,
+		execID, status, resultJSON, durationMs, verified, startedAt, time.Now()); uerr != nil {
+		slog.Error("httpapi: finalize execution status", "error", uerr, "execution_id", execID, "intended_status", status)
+	}
+
+	emitExecutionEvent(ctx, pool, execID, status, map[string]any{
+		"action": action, "target": targetSlug, "duration_ms": durationMs,
+	})
+
+	slog.Info("httpapi: approved action executed",
+		"execution_id", execID, "action", action, "status", status, "duration_ms", durationMs)
+}
+
+// jsonErr builds a valid {"error": "..."} JSON payload for an execution's
+// result column. Always use this instead of fmt.Sprintf'ing JSON by hand —
+// error text and command output routinely contain quotes/backslashes that
+// break a hand-built string and fail the ::jsonb cast.
+func jsonErr(format string, args ...any) []byte {
+	b, _ := json.Marshal(map[string]any{"error": fmt.Sprintf(format, args...)})
+	return b
+}
+
+// resolveTemplate maps a requested template name to one actually present in
+// the host's template cache. Exact match wins; a bare distro hint (e.g.
+// "debian-13" or "debian") matches by prefix; empty picks the newest debian
+// (falling back to any) template available. Returns "" when nothing fits.
+// gatewayPreflightPassed interprets the PREFLIGHT_OK/PREFLIGHT_FAIL markers
+// from the pct_create gateway pre-flight check. Pulled out as its own
+// function (rather than an inline strings.Contains at the call site) so it's
+// unit-testable: a prior version checked for "REACHABLE", which is a
+// substring of "UNREACHABLE" — the check could never actually fail, and it
+// took a live deployment to notice. Exact-match markers plus a test make
+// that specific bug class structurally unable to recur silently.
+func gatewayPreflightPassed(out string) bool {
+	return strings.TrimSpace(out) == "PREFLIGHT_OK"
+}
+
+func resolveTemplate(requested string, available []string) string {
+	if len(available) == 0 {
+		return ""
+	}
+	if requested != "" {
+		for _, a := range available {
+			if a == requested {
+				return a
+			}
+		}
+		for _, a := range available {
+			if strings.HasPrefix(a, requested) {
+				return a
+			}
+		}
+	}
+	// Auto-pick: prefer debian, then the lexically-greatest (newest version).
+	best := ""
+	for _, a := range available {
+		if strings.Contains(a, "debian") && a > best {
+			best = a
+		}
+	}
+	if best != "" {
+		return best
+	}
+	for _, a := range available {
+		if a > best {
+			best = a
+		}
+	}
+	return best
+}

internal/httpapi/agent_activity.go

@@ -0,0 +1,90 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+	"time"
+
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+)
+
+// ─── Agent Activity (stub) ─────────────────────────────────────────────
+
+func (s *Server) QueryAgentActivity(ctx context.Context, request gen.QueryAgentActivityRequestObject) (gen.QueryAgentActivityResponseObject, error) {
+	limit := clampLimit(request.Params.Limit)
+	from := time.Now().Add(-24 * time.Hour)
+	if request.Params.From != nil {
+		from = *request.Params.From
+	}
+	to := time.Now()
+	if request.Params.To != nil {
+		to = *request.Params.To
+	}
+
+	var agentID *string
+	if request.Params.AgentId != nil {
+		a := *request.Params.AgentId
+		agentID = &a
+	}
+	var activityType *string
+	if request.Params.ActivityType != nil {
+		a := string(*request.Params.ActivityType)
+		activityType = &a
+	}
+	var entityID *string
+	if request.Params.EntityId != nil {
+		a := *request.Params.EntityId
+		entityID = &a
+	}
+	var cursorID *int
+	if request.Params.Cursor != nil && *request.Params.Cursor != "" {
+		if id, err := parseIntOrZero(*request.Params.Cursor); err == nil && id > 0 {
+			cursorID = &id
+		}
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT id, ts, agent_id::text, session_id, activity_type, tool_name,
+		       entity_id::text, input_summary, output_summary,
+		       duration_ms, token_count, success, correlation_id
+		FROM agent_activity
+		WHERE ts >= $1 AND ts <= $2
+		  AND ($3::text IS NULL OR agent_id::text = $3)
+		  AND ($4::text IS NULL OR activity_type = $4)
+		  AND ($5::text IS NULL OR entity_id::text = $5)
+		  AND ($6::bigint IS NULL OR id < $6::bigint)
+		ORDER BY id DESC
+		LIMIT $7`,
+		from, to, agentID, activityType, entityID, cursorID, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.AgentActivity{}
+	for rows.Next() {
+		var a gen.AgentActivity
+		if err := rows.Scan(&a.Id, &a.Ts, &a.AgentId, &a.SessionId,
+			&a.ActivityType, &a.ToolName, &a.EntityId,
+			&a.InputSummary, &a.OutputSummary,
+			&a.DurationMs, &a.TokenCount, &a.Success,
+			&a.CorrelationId); err != nil {
+			return nil, err
+		}
+		items = append(items, a)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	var next *string
+	if len(items) > limit {
+		items = items[:limit]
+		lastID := fmt.Sprintf("%d", items[len(items)-1].Id)
+		next = &lastID
+	}
+	if items == nil {
+		items = []gen.AgentActivity{}
+	}
+	return gen.QueryAgentActivity200JSONResponse{Items: items, NextCursor: next}, nil
+}

internal/httpapi/api_test.go

@@ -263,6 +263,20 @@ func TestAPIEndToEnd(t *testing.T) {
 		}
 	})
 
+	// Regression: rel_type is an optional array param (*[]string); when
+	// omitted entirely (not an empty list), passing the nil pointer straight
+	// through to pgx as a query arg panics because pgx can't infer the array
+	// element type from a nil *[]string. root+depth alone must still work.
+	t.Run("graph without rel_type", func(t *testing.T) {
+		rec, body := get(t, h, "/api/v1/graph?root=host:hubris&depth=1", nil)
+		if rec.Code != 200 {
+			t.Fatalf("status %d", rec.Code)
+		}
+		if len(body["nodes"].([]any)) < 2 {
+			t.Errorf("graph too small: %d nodes", len(body["nodes"].([]any)))
+		}
+	})
+
 	t.Run("ontology", func(t *testing.T) {
 		rec, body := get(t, h, "/api/v1/ontology", nil)
 		if rec.Code != 200 {

internal/httpapi/approval_rules.go

@@ -0,0 +1,162 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+	"strings"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+)
+
+// ─── Approval Rules (Policy) ───────────────────────────────────────────
+
+func (s *Server) ListApprovalRules(ctx context.Context, req gen.ListApprovalRulesRequestObject) (gen.ListApprovalRulesResponseObject, error) {
+	rows, err := s.pool.Query(ctx, `
+		SELECT id, entity_type, action, risk_class, autonomy_level,
+		       COALESCE((SELECT slug FROM entities WHERE id = scope_entity), ''),
+		       version, updated_at
+		FROM approval_rules ORDER BY entity_type, action`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.ApprovalRule{}
+	for rows.Next() {
+		var rule gen.ApprovalRule
+		var scopeSlug string
+		if err := rows.Scan(&rule.Id, &rule.EntityType, &rule.Action,
+			&rule.RiskClass, &rule.AutonomyLevel, &scopeSlug,
+			&rule.Version); err != nil {
+			return nil, err
+		}
+		if scopeSlug != "" {
+			rule.ScopeEntity = &scopeSlug
+		}
+		items = append(items, rule)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.ApprovalRule{}
+	}
+	return gen.ListApprovalRules200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) CreateApprovalRule(ctx context.Context, req gen.CreateApprovalRuleRequestObject) (gen.CreateApprovalRuleResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := uuid.NewV7()
+	if err != nil {
+		return nil, err
+	}
+
+	var scopeEntity *uuid.UUID
+	if req.Body.ScopeEntity != nil && *req.Body.ScopeEntity != "" {
+		se, rerr := s.resolveEntityID(ctx, *req.Body.ScopeEntity)
+		if rerr != nil {
+			return nil, rerr
+		}
+		scopeEntity = &se
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	_, err = tx.Exec(ctx, `
+		INSERT INTO approval_rules (id, entity_type, action, risk_class, autonomy_level, scope_entity)
+		VALUES ($1, $2, $3, $4, $5, $6)`,
+		id, req.Body.EntityType, req.Body.Action, req.Body.RiskClass,
+		string(req.Body.AutonomyLevel), scopeEntity)
+	if err != nil {
+		if strings.Contains(err.Error(), "unique") || strings.Contains(err.Error(), "duplicate") {
+			return nil, fmt.Errorf("%w: rule for %s/%s already exists", domain.ErrAlreadyExists,
+				coalesceStr(req.Body.EntityType, "*"), req.Body.Action)
+		}
+		return nil, err
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "create",
+		&id, "POST", "/api/v1/policy/approval-rules", "",
+		nil,
+		map[string]any{"action": req.Body.Action, "risk_class": req.Body.RiskClass}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	// Return 202 pending approval (dual-control).
+	return gen.CreateApprovalRule202JSONResponse{}, nil
+}
+
+func (s *Server) PatchApprovalRule(ctx context.Context, req gen.PatchApprovalRuleRequestObject) (gen.PatchApprovalRuleResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	var scopeEntity *uuid.UUID
+	if req.Body.ScopeEntity != nil && *req.Body.ScopeEntity != "" {
+		se, rerr := s.resolveEntityID(ctx, *req.Body.ScopeEntity)
+		if rerr != nil {
+			return nil, rerr
+		}
+		scopeEntity = &se
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	result, err := tx.Exec(ctx, `
+		UPDATE approval_rules
+		SET entity_type = COALESCE($2, entity_type),
+		    action = COALESCE($3, action),
+		    risk_class = COALESCE($4, risk_class),
+		    autonomy_level = COALESCE($5, autonomy_level),
+		    scope_entity = COALESCE($6, scope_entity),
+		    version = version + 1,
+		    updated_at = now()
+		WHERE id = $1`,
+		id, req.Body.EntityType, req.Body.Action, req.Body.RiskClass,
+		string(req.Body.AutonomyLevel), scopeEntity)
+	if err != nil {
+		return nil, err
+	}
+	if result.RowsAffected() == 0 {
+		return nil, fmt.Errorf("%w: approval rule %s", domain.ErrNotFound, req.Id)
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "patch",
+		&id, "PATCH", "/api/v1/policy/approval-rules/"+req.Id, "",
+		nil,
+		map[string]any{"action": req.Body.Action}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchApprovalRule202JSONResponse{}, nil
+}

internal/httpapi/approvals.go

@@ -0,0 +1,287 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"log/slog"
+	"time"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/dtoro/oikos/internal/safego"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// ─── Approvals ─────────────────────────────────────────────────────────
+
+func (s *Server) ListApprovals(ctx context.Context, req gen.ListApprovalsRequestObject) (gen.ListApprovalsResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+	var status *string
+	if req.Params.Status != nil {
+		s := string(*req.Params.Status)
+		status = &s
+	}
+	var kind *string
+	if req.Params.Kind != nil {
+		k := string(*req.Params.Kind)
+		kind = &k
+	}
+	rows, err := s.pool.Query(ctx, `
+		SELECT a.entity_id, a.action, a.risk_class, a.kind, a.payload,
+		       a.status, a.expires_at, a.decided_at, a.decided_by::text,
+		       a.created_at, e.slug
+		FROM approvals a
+		JOIN entities e ON e.id = COALESCE(a.subject_entity_id, a.entity_id)
+		WHERE ($1::text IS NULL OR a.status = $1)
+		  AND ($2::text IS NULL OR a.kind = $2)
+		  AND ($3::text IS NULL OR e.slug > $3)
+		ORDER BY e.slug
+		LIMIT $4`,
+		status, kind, req.Params.Cursor, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Approval{}
+	for rows.Next() {
+		var a gen.Approval
+		var payloadBytes []byte
+		var decidedBy *string
+		if err := rows.Scan(&a.Id, &a.Action, &a.RiskClass, &a.Kind, &payloadBytes,
+			&a.Status, &a.ExpiresAt, &a.DecidedAt, &decidedBy,
+			&a.CreatedAt, &a.Slug); err != nil {
+			return nil, err
+		}
+		a.DecidedBy = decidedBy
+		var payload map[string]any
+		if len(payloadBytes) > 0 && json.Unmarshal(payloadBytes, &payload) == nil {
+			a.Payload = &payload
+		}
+		items = append(items, a)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	var next *string
+	if len(items) > limit {
+		items = items[:limit]
+		next = &items[len(items)-1].Slug
+	}
+	if items == nil {
+		items = []gen.Approval{}
+	}
+	return gen.ListApprovals200JSONResponse{Items: items, NextCursor: next}, nil
+}
+
+func (s *Server) DecideApproval(ctx context.Context, req gen.DecideApprovalRequestObject) (gen.DecideApprovalResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	actorType, actor := actorInfo(ctx)
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	q := sqlcgen.New(tx)
+
+	// Verify HMAC token if provided (single-use, S5).
+	if req.Body.Token != nil && *req.Body.Token != "" {
+		var tokenHash *string
+		var apprStatus string
+		var expiresAt time.Time
+		err := tx.QueryRow(ctx,
+			"SELECT token_hash, status, expires_at FROM approvals WHERE entity_id = $1",
+			id).Scan(&tokenHash, &apprStatus, &expiresAt)
+		if err != nil || tokenHash == nil {
+			return nil, fmt.Errorf("%w: approval not found", domain.ErrNotFound)
+		}
+		if apprStatus != "pending" {
+			return nil, fmt.Errorf("%w: approval already decided", domain.ErrInvalidTransition)
+		}
+		if expiresAt.Before(time.Now()) {
+			return nil, fmt.Errorf("%w: approval token expired", domain.ErrInvalidTransition)
+		}
+		if *tokenHash != hashToken(*req.Body.Token) {
+			return nil, fmt.Errorf("%w: invalid approval token", domain.ErrInvalidInput)
+		}
+	}
+
+	// Map decision to status.
+	var status string
+	switch req.Body.Decision {
+	case gen.Approve:
+		status = "approved"
+	case gen.Deny:
+		status = "denied"
+	case gen.Revoke:
+		status = "revoked"
+	default:
+		return nil, fmt.Errorf("%w: invalid decision %q", domain.ErrInvalidInput, req.Body.Decision)
+	}
+
+	if err := q.UpdateApprovalStatus(ctx, sqlcgen.UpdateApprovalStatusParams{
+		EntityID: id,
+		Status:   status,
+	}); err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: approval %s not found or already decided", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+
+	// Re-read approval.
+	app, err := q.GetApprovalByID(ctx, id)
+	if err != nil {
+		return nil, err
+	}
+
+	approval := approvalToGen(app)
+
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "decide",
+		&id, "POST", "/api/v1/approvals/"+req.Id+"/decision", "",
+		nil,
+		map[string]any{"decision": status}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	// Emit for SSE fan-out (in-tx; NOTIFY fires post-commit).
+	if evErr := observability.Event(ctx, q, "approval.decided", &id, "info", "api", "",
+		map[string]any{"decision": status, "actor": actor}); evErr != nil {
+		return nil, evErr
+	}
+
+	// On approve: execute the linked gated command.
+	if status == "approved" {
+		var execID, targetID uuid.UUID
+		var actionStr, targetSlug, riskClass string
+		err := tx.QueryRow(ctx, `
+			SELECT e.entity_id, e.target_entity_id, e.action, e.risk_class
+			FROM executions e
+			WHERE e.approval_id = $1 AND e.status = 'pending_approval'
+			LIMIT 1`, id).Scan(&execID, &targetID, &actionStr, &riskClass)
+		if err == nil {
+			// Resolve target entity slug from targetID.
+			_ = tx.QueryRow(ctx, "SELECT slug FROM entities WHERE id = $1", targetID).Scan(&targetSlug)
+
+			safego.Go("httpapi:executeApprovedAction", func() {
+				executeApprovedAction(context.Background(), s.pool, execID, targetSlug, actionStr)
+			})
+			// Status only — risk_class was set correctly at request time
+			// (e.g. by policy.ClassifyCommand for `run`); overwriting it to
+			// a hardcoded 'config_mutation' here corrupted the audit ledger
+			// for every other risk class, including destructive.
+			_, _ = tx.Exec(ctx, `UPDATE executions SET status = 'approved' WHERE entity_id = $1`, execID)
+
+			// Approving a plan step — by ANY route (this endpoint backs both
+			// the chat Approve button and chat-assent) — opens/extends the
+			// agent's assent window. This is the scope gate the Nomos
+			// auto-continuation worker checks: with the window open, the
+			// finished execution's result is fed back to the agent so it runs
+			// the plan to completion. Without opening it here, approving via
+			// the button (instead of typing "go ahead") would silently not
+			// auto-continue.
+			var agentID *uuid.UUID
+			if qerr := tx.QueryRow(ctx, "SELECT agent_id FROM executions WHERE entity_id = $1", execID).Scan(&agentID); qerr == nil && agentID != nil {
+				expires := time.Now().Add(30 * time.Minute).UTC().Format(time.RFC3339)
+				_, _ = tx.Exec(ctx, `INSERT INTO autonomy_settings (key, value) VALUES ($1, $2)
+					ON CONFLICT (key) DO UPDATE SET value = $2`, "assent_window.agent:"+agentID.String(), expires)
+
+				// Approving a DESTRUCTIVE step via the button is exactly as
+				// explicit as a typed "I confirm" — the operator affirmatively
+				// clicked Approve on a card that said DESTRUCTIVE. Open the
+				// same short, target-scoped destructive window chat-assent's
+				// typed-confirm path opens, for parity: a multi-step
+				// destructive recovery (stop, then destroy) shouldn't need a
+				// fresh confirmation per click any more than it needs one per
+				// typed phrase.
+				if riskClass == "destructive" && targetSlug != "" {
+					dExpires := time.Now().Add(15 * time.Minute).UTC().Format(time.RFC3339)
+					_, _ = tx.Exec(ctx, `INSERT INTO autonomy_settings (key, value) VALUES ($1, $2)
+						ON CONFLICT (key) DO UPDATE SET value = $2`,
+						"destructive_window.agent:"+agentID.String()+".target:"+targetSlug, dExpires)
+				}
+			}
+
+			slog.Info("httpapi: approved execution queued",
+				"execution_id", execID, "target", targetSlug, "action", actionStr)
+		} else {
+			slog.Warn("httpapi: no pending execution found for approval", "approval_id", id, "error", err)
+		}
+	} else {
+		// Denied/revoked: reflect it on the linked execution too. Previously
+		// only the approvals row changed, so the execution stayed
+		// 'pending_approval' forever — any UI/poller reading execution
+		// status (not approval status) never saw the decision.
+		_, _ = tx.Exec(ctx, `UPDATE executions SET status = $2, completed_at = now() WHERE approval_id = $1 AND status = 'pending_approval'`, id, status)
+	}
+
+	// If this execution belongs to a nomos session, flip it out of
+	// awaiting_input — the counterpart to classifyAndGate flipping it IN
+	// the moment the approval was created (internal/mcp/server.go's
+	// markSessionAwaitingApproval). Runs for all three decisions (approve/
+	// deny/revoke): each one is an operator answer to "what do I do about
+	// this?", same as answerQuestion's unconditional resume-to-executing
+	// (cmd/nomos/store.go) for a session_questions answer.
+	var awaitingSessionID string
+	_ = tx.QueryRow(ctx, `
+		SELECT pe.session_id FROM nomos_plan_executions pe
+		JOIN executions ex ON ex.entity_id = pe.execution_id
+		WHERE ex.approval_id = $1
+		LIMIT 1`, id).Scan(&awaitingSessionID)
+	if awaitingSessionID != "" {
+		if rtag, rerr := tx.Exec(ctx, `
+			UPDATE agent_sessions SET status = 'executing', last_active_at = now()
+			WHERE id = $1 AND status = 'awaiting_input'`, awaitingSessionID); rerr == nil && rtag.RowsAffected() > 0 {
+			var taskEntID *uuid.UUID
+			var e uuid.UUID
+			if qerr := tx.QueryRow(ctx, `SELECT entity_id FROM agent_sessions WHERE id = $1`, awaitingSessionID).Scan(&e); qerr == nil && e != uuid.Nil {
+				taskEntID = &e
+			}
+			_ = observability.Event(ctx, q, "task.status", taskEntID, "info", "api", awaitingSessionID,
+				map[string]any{"status": "executing", "reason": "approval_decided", "decision": status})
+		}
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.DecideApproval200JSONResponse(approval), nil
+}
+
+func approvalToGen(a sqlcgen.Approval) gen.Approval {
+	app := gen.Approval{
+		Id:        a.EntityID,
+		Action:    a.Action,
+		RiskClass: a.RiskClass,
+		Kind:      gen.ApprovalKind(a.Kind),
+		Status:    gen.ApprovalStatus(a.Status),
+		ExpiresAt: a.ExpiresAt,
+		DecidedAt: a.DecidedAt,
+		CreatedAt: a.CreatedAt,
+	}
+	if a.DecidedBy != nil {
+		s := a.DecidedBy.String()
+		app.DecidedBy = &s
+	}
+	var payload map[string]any
+	if len(a.Payload) > 0 && json.Unmarshal(a.Payload, &payload) == nil && len(payload) > 0 {
+		app.Payload = &payload
+	}
+	return app
+}

internal/httpapi/audit.go

@@ -0,0 +1,20 @@
+package httpapi
+
+import (
+	"net/http"
+
+	"github.com/dtoro/oikos/internal/audit"
+)
+
+// serveAuditDrift returns a read-only DB-side drift report: orphan check
+// entities, checks on retired targets, probes stuck down/unknown, unmonitored
+// declared types, and dangling edges. Companion to the knowledge-graph-audit
+// skill. Live-infra discovery (pct/docker/certs) is a follow-up.
+func (s *Server) serveAuditDrift(w http.ResponseWriter, req *http.Request) {
+	findings, summary := audit.Report(req.Context(), s.pool)
+	writeJSON(w, map[string]any{
+		"findings": findings,
+		"summary":  summary,
+		"note":     "read-only DB drift report; live-infra discovery (pct/docker/certs) is a follow-up",
+	})
+}

internal/httpapi/autonomy.go

@@ -0,0 +1,103 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+)
+
+// ─── Autonomy Settings ─────────────────────────────────────────────────
+
+func (s *Server) GetAutonomySettings(ctx context.Context, req gen.GetAutonomySettingsRequestObject) (gen.GetAutonomySettingsResponseObject, error) {
+	rows, err := s.pool.Query(ctx, `SELECT key, value, version, updated_at FROM autonomy_settings ORDER BY key`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.AutonomySetting{}
+	for rows.Next() {
+		var as gen.AutonomySetting
+		if err := rows.Scan(&as.Key, &as.Value, &as.Version, &as.UpdatedAt); err != nil {
+			return nil, err
+		}
+		items = append(items, as)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.AutonomySetting{}
+	}
+	return gen.GetAutonomySettings200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) PatchAutonomySettings(ctx context.Context, req gen.PatchAutonomySettingsRequestObject) (gen.PatchAutonomySettingsResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	for key, value := range *req.Body {
+		_, err := tx.Exec(ctx, `
+			INSERT INTO autonomy_settings (key, value, version, updated_at)
+			VALUES ($1, $2, 1, now())
+			ON CONFLICT (key)
+			DO UPDATE SET value = EXCLUDED.value, version = autonomy_settings.version + 1, updated_at = now()`,
+			key, value)
+		if err != nil {
+			return nil, err
+		}
+	}
+
+	// Re-read all settings.
+	rows, err := tx.Query(ctx, `SELECT key, value, version, updated_at FROM autonomy_settings ORDER BY key`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.AutonomySetting{}
+	for rows.Next() {
+		var as gen.AutonomySetting
+		if err := rows.Scan(&as.Key, &as.Value, &as.Version, &as.UpdatedAt); err != nil {
+			return nil, err
+		}
+		items = append(items, as)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "patch",
+		nil, "PATCH", "/api/v1/policy/autonomy", "",
+		nil,
+		map[string]any{"keys": keysOfMap(*req.Body)}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchAutonomySettings200JSONResponse{Items: items}, nil
+}
+
+// keysOfMap returns the keys of a map[string]string.
+func keysOfMap(m map[string]string) []string {
+	keys := make([]string, 0, len(m))
+	for k := range m {
+		keys = append(keys, k)
+	}
+	return keys
+}

internal/httpapi/checks.go

@@ -0,0 +1,324 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"strings"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// ─── Checks ────────────────────────────────────────────────────────────
+
+func (s *Server) ListChecks(ctx context.Context, req gen.ListChecksRequestObject) (gen.ListChecksResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+	rows, err := s.pool.Query(ctx, `
+		SELECT cd.entity_id, e.slug, cd.kind,
+		       COALESCE(te.slug, '') AS target_slug, cd.target_type,
+		       cd.config, cd.interval_s, cd.timeout_s, cd.zone, cd.enabled,
+		       e.version, cd.last_health, cd.last_run_at
+		FROM check_defs cd
+		JOIN entities e ON e.id = cd.entity_id
+		LEFT JOIN entities te ON te.id = cd.target_id
+		WHERE ($1::text IS NULL OR cd.kind = $1)
+		  AND ($2::text IS NULL OR te.slug = $2)
+		  AND ($3::bool IS NULL OR cd.enabled = $3)
+		  AND ($4::text IS NULL OR e.slug > $4)
+		ORDER BY e.slug
+		LIMIT $5`,
+		req.Params.Kind, req.Params.Target, req.Params.Enabled, req.Params.Cursor, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Check{}
+	for rows.Next() {
+		var c gen.Check
+		var targetSlug string
+		var configBytes []byte
+		// last_health is what turns a check list from configuration into an
+		// explanation: an entity's health is the worst of these, so this is
+		// the field that says which probe is responsible.
+		var lastHealth *string
+		if err := rows.Scan(&c.Id, &c.Slug, &c.Kind, &targetSlug, &c.TargetType,
+			&configBytes, &c.IntervalS, &c.TimeoutS, &c.Zone, &c.Enabled, &c.Version,
+			&lastHealth, &c.LastRunAt); err != nil {
+			return nil, err
+		}
+		if lastHealth != nil {
+			h := gen.CheckLastHealth(*lastHealth)
+			c.LastHealth = &h
+		}
+		if targetSlug != "" {
+			c.Target = &targetSlug
+		}
+		var config map[string]any
+		if len(configBytes) > 0 && json.Unmarshal(configBytes, &config) == nil && len(config) > 0 {
+			c.Config = &config
+		}
+		items = append(items, c)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	var next *string
+	if len(items) > limit {
+		items = items[:limit]
+		next = &items[len(items)-1].Slug
+	}
+	if items == nil {
+		items = []gen.Check{}
+	}
+	return gen.ListChecks200JSONResponse{Items: items, NextCursor: next}, nil
+}
+
+func (s *Server) CreateCheck(ctx context.Context, req gen.CreateCheckRequestObject) (gen.CreateCheckResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := uuid.NewV7()
+	if err != nil {
+		return nil, err
+	}
+
+	slug := req.Body.Slug
+	if slug == "" {
+		slug = "check:" + string(req.Body.Kind) + ":" + uuid.New().String()[:8]
+	}
+
+	// Resolve target if provided.
+	var targetID *uuid.UUID
+	if req.Body.Target != nil && *req.Body.Target != "" {
+		tid, rerr := s.resolveEntityID(ctx, *req.Body.Target)
+		if rerr != nil {
+			return nil, rerr
+		}
+		targetID = &tid
+	}
+
+	intervalS := int32(300)
+	if req.Body.IntervalS != nil {
+		intervalS = int32(*req.Body.IntervalS)
+	}
+	timeoutS := int32(30)
+	if req.Body.TimeoutS != nil {
+		timeoutS = int32(*req.Body.TimeoutS)
+	}
+	enabled := true
+	if req.Body.Enabled != nil {
+		enabled = *req.Body.Enabled
+	}
+
+	configJSON := []byte("{}")
+	if req.Body.Config != nil {
+		configJSON, _ = json.Marshal(req.Body.Config)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	q := sqlcgen.New(tx)
+
+	// Create the entity row (checks are entities).
+	entity, err := q.InsertEntity(ctx, sqlcgen.InsertEntityParams{
+		ID:         id,
+		Slug:       slug,
+		Type:       "check",
+		Name:       slug,
+		Attributes: []byte("{}"),
+	})
+	if err != nil {
+		if strings.Contains(err.Error(), "unique") || strings.Contains(err.Error(), "duplicate") {
+			return nil, fmt.Errorf("%w: check %q already exists", domain.ErrAlreadyExists, slug)
+		}
+		return nil, err
+	}
+
+	if err := q.InsertCheckDef(ctx, sqlcgen.InsertCheckDefParams{
+		EntityID:   id,
+		TargetID:   targetID,
+		TargetType: req.Body.TargetType,
+		Kind:       string(req.Body.Kind),
+		Config:     configJSON,
+		IntervalS:  intervalS,
+		TimeoutS:   timeoutS,
+		Zone:       req.Body.Zone,
+		Enabled:    enabled,
+	}); err != nil {
+		return nil, err
+	}
+
+	// Build response Check.
+	check := gen.Check{
+		Id:         id,
+		Slug:       entity.Slug,
+		Kind:       gen.CheckKind(req.Body.Kind),
+		IntervalS:  int(intervalS),
+		TimeoutS:   int(timeoutS),
+		Enabled:    enabled,
+		TargetType: req.Body.TargetType,
+		Zone:       req.Body.Zone,
+		Version:    int(entity.Version),
+	}
+	if req.Body.Config != nil {
+		check.Config = req.Body.Config
+	}
+	if targetID != nil && req.Body.Target != nil {
+		check.Target = req.Body.Target
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "create",
+		&id, "POST", "/api/v1/checks", "",
+		nil,
+		map[string]any{"kind": req.Body.Kind, "slug": slug}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.CreateCheck201JSONResponse(check), nil
+}
+
+func (s *Server) PatchCheck(ctx context.Context, req gen.PatchCheckRequestObject) (gen.PatchCheckResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	// Parse If-Match
+	ifMatch := strings.Trim(req.Params.IfMatch, `"`)
+	expectedVersion, err := parseIntIfMatch(ifMatch)
+	if err != nil {
+		return nil, err
+	}
+	_ = expectedVersion // check_defs don't track version via If-Match today, but we validate the header is present
+
+	if ifMatch == "" {
+		return nil, fmt.Errorf("%w: invalid If-Match header", domain.ErrInvalidInput)
+	}
+
+	// Get current check def
+	current, err := sqlcgen.New(s.pool).GetCheckDef(ctx, id)
+	if err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: check %s", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	// Apply patch.
+	if req.Body.Config != nil {
+		current.Config, _ = json.Marshal(req.Body.Config)
+	}
+	if req.Body.IntervalS != nil {
+		current.IntervalS = int32(*req.Body.IntervalS)
+	}
+	if req.Body.TimeoutS != nil {
+		current.TimeoutS = int32(*req.Body.TimeoutS)
+	}
+	if req.Body.Enabled != nil {
+		current.Enabled = *req.Body.Enabled
+	}
+
+	if err := sqlcgen.New(tx).UpdateCheckDef(ctx, sqlcgen.UpdateCheckDefParams{
+		EntityID:   id,
+		Kind:       current.Kind,
+		Config:     current.Config,
+		IntervalS:  current.IntervalS,
+		TimeoutS:   current.TimeoutS,
+		TargetID:   current.TargetID,
+		TargetType: current.TargetType,
+		Zone:       current.Zone,
+		Enabled:    current.Enabled,
+	}); err != nil {
+		return nil, err
+	}
+
+	// Re-read to get updated timestamp.
+	updated, err := sqlcgen.New(tx).GetCheckDef(ctx, id)
+	if err != nil {
+		return nil, err
+	}
+
+	check := checkDefToGen(updated)
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "patch",
+		&id, "PATCH", "/api/v1/checks/"+req.Id, "",
+		nil,
+		map[string]any{"enabled": updated.Enabled}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchCheck200JSONResponse(check), nil
+}
+
+func checkDefToGen(cd sqlcgen.CheckDef) gen.Check {
+	c := gen.Check{
+		Id:         cd.EntityID,
+		Kind:       gen.CheckKind(cd.Kind),
+		IntervalS:  int(cd.IntervalS),
+		TimeoutS:   int(cd.TimeoutS),
+		Enabled:    cd.Enabled,
+		TargetType: cd.TargetType,
+		Zone:       cd.Zone,
+	}
+	var config map[string]any
+	if len(cd.Config) > 0 && json.Unmarshal(cd.Config, &config) == nil && len(config) > 0 {
+		c.Config = &config
+	}
+	// Carried through so toggling a check does not blank its verdict in the
+	// UI — the entity window renders last_health to explain which probe is
+	// responsible for an entity's health, and a patch response missing it
+	// would erase that until the next poll.
+	c.LastRunAt = cd.LastRunAt
+	if cd.LastHealth != nil {
+		h := gen.CheckLastHealth(*cd.LastHealth)
+		c.LastHealth = &h
+	}
+	return c
+}
+
+// parseIntIfMatch parses an integer from a raw If-Match header value (with quotes stripped).
+func parseIntIfMatch(s string) (int, error) {
+	if s == "" {
+		return 0, fmt.Errorf("empty version")
+	}
+	var v int
+	for _, c := range s {
+		if c < '0' || c > '9' {
+			return 0, fmt.Errorf("invalid version: %q", s)
+		}
+		v = v*10 + int(c-'0')
+	}
+	return v, nil
+}

internal/httpapi/classifications.go

@@ -0,0 +1,85 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/google/uuid"
+)
+
+// ─── Classifications ───────────────────────────────────────────────────
+
+func (s *Server) ListClassifications(ctx context.Context, req gen.ListClassificationsRequestObject) (gen.ListClassificationsResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+	var route *string
+	if req.Params.Route != nil {
+		r := string(*req.Params.Route)
+		route = &r
+	}
+	rows, err := s.pool.Query(ctx, `
+		SELECT c.entity_id, c.signal_entity_id, c.target_entity_id, c.action,
+		       c.recommended_action, c.risk_class, c.route, c.blast_radius,
+		       c.pattern_confidence, c.skill_id, c.autonomy_check, c.reasoning,
+		       c.correlation_id, c.created_at,
+		       e.slug, COALESCE(se.slug, '') AS signal_slug, COALESCE(te.slug, '') AS target_slug
+		FROM classifications c
+		LEFT JOIN entities e ON e.id = c.entity_id
+		LEFT JOIN entities se ON se.id = c.signal_entity_id
+		LEFT JOIN entities te ON te.id = c.target_entity_id
+		WHERE ($1::text IS NULL OR c.route = $1)
+		  AND ($2::text IS NULL OR e.slug > $2)
+		ORDER BY e.slug
+		LIMIT $3`,
+		route, req.Params.Cursor, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Classification{}
+	for rows.Next() {
+		var cls gen.Classification
+		var recActionJSON []byte
+		var reasoningJSON []byte
+		var blastRadius []uuid.UUID
+		var signalSlug, targetSlug string
+		if err := rows.Scan(&cls.Id, &cls.SignalId, &targetSlug, &cls.Action,
+			&recActionJSON, &cls.RiskClass, &cls.Route, &blastRadius,
+			&cls.PatternConfidence, &cls.SkillId, &cls.AutonomyCheck, &reasoningJSON,
+			&cls.CorrelationId, &cls.CreatedAt,
+			&cls.Target, &signalSlug, &targetSlug); err != nil {
+			return nil, err
+		}
+		if targetSlug != "" {
+			cls.Target = &targetSlug
+		}
+		var reasoning map[string]any
+		if json.Unmarshal(reasoningJSON, &reasoning) == nil {
+			cls.Reasoning = reasoning
+		}
+		if len(blastRadius) > 0 {
+			br := make([]string, len(blastRadius))
+			for i, id := range blastRadius {
+				br[i] = id.String()
+			}
+			cls.BlastRadius = &br
+		}
+		items = append(items, cls)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	var next *string
+	if len(items) > limit {
+		items = items[:limit]
+		if items[len(items)-1].Target != nil {
+			next = items[len(items)-1].Target
+		}
+	}
+	if items == nil {
+		items = []gen.Classification{}
+	}
+	return gen.ListClassifications200JSONResponse{Items: items, NextCursor: next}, nil
+}

internal/httpapi/default_checks.go

@@ -3,11 +3,22 @@ package httpapi
 import (
 	"context"
 
-	"github.com/dtoro/oikos/internal/checkdefaults"
+	"github.com/dtoro/oikos/internal/db"
 	"github.com/google/uuid"
 	"github.com/jackc/pgx/v5"
 )
 
-func ensureDefaultChecks(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, slug, entityType string, attrsJSON []byte) {
-	checkdefaults.Ensure(ctx, tx, entityID, slug, entityType, attrsJSON)
+// ensureDefaultChecks derives an entity's default checks from the monitoring
+// kinds its type declares. Thin wrapper over the shared db.EnsureEntityChecks
+// hook so the HTTP create/patch paths and the MCP entity-mutation tools stay
+// in lockstep.
+//
+// Note the ordering caveat (carried from db.LoadTypeTree / checkdefaults.Ensure):
+// an entity created through the API usually has no edges yet, so a type whose
+// address comes from its host (a service) will produce no checks on this pass.
+// That gap is real and deliberately visible — coverageSweep reports it, and
+// the next inventory ingest fills it in once the hosting edge exists.
+func ensureDefaultChecks(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, slug, entityType, name string, attrsJSON []byte) error {
+	_, err := db.EnsureEntityChecks(ctx, tx, entityID, slug, entityType, name, attrsJSON)
+	return err
 }

internal/httpapi/entity_types.go

@@ -0,0 +1,162 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"strings"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+)
+
+// ─── Entity Types (Ontology) ───────────────────────────────────────────
+
+func (s *Server) CreateEntityType(ctx context.Context, req gen.CreateEntityTypeRequestObject) (gen.CreateEntityTypeResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	isAbstract := false
+	if req.Body.IsAbstract != nil {
+		isAbstract = *req.Body.IsAbstract
+	}
+
+	attrsSchemaJSON := []byte("null")
+	if req.Body.AttributeSchema != nil {
+		attrsSchemaJSON, _ = json.Marshal(req.Body.AttributeSchema)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	_, err = tx.Exec(ctx, `
+		INSERT INTO entity_types (name, parent_type, is_abstract, domain, layer, description, lifecycle_id, attribute_schema, status)
+		VALUES ($1, $2, $3, $4, $5, $6, $7, $8, 'active')`,
+		req.Body.Name, req.Body.ParentType, isAbstract, req.Body.Domain,
+		string(req.Body.Layer), req.Body.Description, req.Body.LifecycleId, attrsSchemaJSON)
+	if err != nil {
+		if strings.Contains(err.Error(), "unique") || strings.Contains(err.Error(), "duplicate") {
+			return nil, fmt.Errorf("%w: entity type %q already exists", domain.ErrAlreadyExists, req.Body.Name)
+		}
+		return nil, err
+	}
+
+	// Re-read.
+	var et gen.EntityType
+	var schemaBytes []byte
+	err = tx.QueryRow(ctx, `
+		SELECT name, parent_type, is_abstract, domain, layer, description,
+		       lifecycle_id, attribute_schema, schema_version, status
+		FROM entity_types WHERE name = $1`, req.Body.Name).
+		Scan(&et.Name, &et.ParentType, &et.IsAbstract, &et.Domain, &et.Layer,
+			&et.Description, &et.LifecycleId, &schemaBytes, &et.SchemaVersion, &et.Status)
+	if err != nil {
+		return nil, err
+	}
+	var schema map[string]any
+	if len(schemaBytes) > 0 && json.Unmarshal(schemaBytes, &schema) == nil && schema != nil {
+		et.AttributeSchema = &schema
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "create",
+		nil, "POST", "/api/v1/ontology/entity-types", "",
+		nil,
+		map[string]any{"name": req.Body.Name, "domain": req.Body.Domain}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.CreateEntityType201JSONResponse(et), nil
+}
+
+func (s *Server) PatchEntityType(ctx context.Context, req gen.PatchEntityTypeRequestObject) (gen.PatchEntityTypeResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	// Build dynamic update.
+	sets := []string{}
+	args := []any{}
+	argIdx := 2
+
+	if req.Body.Description != nil {
+		sets = append(sets, fmt.Sprintf("description = $%d", argIdx))
+		args = append(args, *req.Body.Description)
+		argIdx++
+	}
+	if req.Body.Status != nil {
+		sets = append(sets, fmt.Sprintf("status = $%d", argIdx))
+		args = append(args, string(*req.Body.Status))
+		argIdx++
+	}
+	if req.Body.AttributeSchema != nil {
+		schemaJSON, _ := json.Marshal(req.Body.AttributeSchema)
+		sets = append(sets, fmt.Sprintf("attribute_schema = $%d", argIdx))
+		args = append(args, schemaJSON)
+		argIdx++
+	}
+
+	if len(sets) == 0 {
+		return nil, fmt.Errorf("%w: no fields to update", domain.ErrInvalidInput)
+	}
+
+	sets = append(sets, "schema_version = schema_version + 1, updated_at = now()")
+
+	query := fmt.Sprintf(`UPDATE entity_types SET %s WHERE name = $1`, strings.Join(sets, ", "))
+	finalArgs := append([]any{req.Name}, args...)
+
+	result, err := tx.Exec(ctx, query, finalArgs...)
+	if err != nil {
+		return nil, err
+	}
+	if result.RowsAffected() == 0 {
+		return nil, fmt.Errorf("%w: entity type %q", domain.ErrNotFound, req.Name)
+	}
+
+	// Re-read.
+	var et gen.EntityType
+	var schemaBytes []byte
+	err = tx.QueryRow(ctx, `
+		SELECT name, parent_type, is_abstract, domain, layer, description,
+		       lifecycle_id, attribute_schema, schema_version, status
+		FROM entity_types WHERE name = $1`, req.Name).
+		Scan(&et.Name, &et.ParentType, &et.IsAbstract, &et.Domain, &et.Layer,
+			&et.Description, &et.LifecycleId, &schemaBytes, &et.SchemaVersion, &et.Status)
+	if err != nil {
+		return nil, err
+	}
+	var schema map[string]any
+	if len(schemaBytes) > 0 && json.Unmarshal(schemaBytes, &schema) == nil && schema != nil {
+		et.AttributeSchema = &schema
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "patch",
+		nil, "PATCH", "/api/v1/ontology/entity-types/"+req.Name, "",
+		nil,
+		map[string]any{"status": req.Body.Status}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchEntityType200JSONResponse(et), nil
+}

internal/httpapi/execution_logs.go

@@ -0,0 +1,55 @@
+package httpapi
+
+import (
+	"encoding/json"
+	"net/http"
+	"strconv"
+	"strings"
+
+	"github.com/dtoro/oikos/internal/execlog"
+	"github.com/go-chi/chi/v5"
+	"github.com/google/uuid"
+)
+
+// serveExecutionLogs returns an execution's streamed command output.
+//
+// Registered as a carve-out rather than through the OpenAPI codegen for the
+// same reason as /activity/recent: it is a recency-ordered projection with no
+// schema type yet. Without this the execution_logs rows would be write-only —
+// which is the exact shape of the bugs this whole change set has been about.
+func (s *Server) serveExecutionLogs(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	rawID := chi.URLParam(req, "id")
+	execID, err := uuid.Parse(rawID)
+	if err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid execution id", rawID)
+		return
+	}
+
+	limit := 1000
+	if l := req.URL.Query().Get("limit"); l != "" {
+		if n, perr := strconv.Atoi(l); perr == nil && n > 0 && n <= 5000 {
+			limit = n
+		}
+	}
+
+	chunks, err := execlog.Read(ctx, s.pool, execID, limit)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+
+	// Also hand back the concatenation, since that is what a caller tailing
+	// output actually wants to render.
+	var combined strings.Builder
+	for _, c := range chunks {
+		combined.WriteString(c.Chunk)
+	}
+
+	w.Header().Set("Content-Type", "application/json")
+	_ = json.NewEncoder(w).Encode(map[string]any{
+		"items":    chunks,
+		"combined": combined.String(),
+	})
+}

internal/httpapi/executions.go

@@ -0,0 +1,321 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"strings"
+	"time"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// ─── Executions ────────────────────────────────────────────────────────
+
+// ListExecutions returns executions newest-first.
+//
+// The target/action/correlation_id filters are declared in the OpenAPI spec and
+// generated into the request struct, but were never bound — so
+// `GET /executions?target=<id>` silently returned the first page of the whole
+// fleet. Ordering was by target slug, which is neither useful for a history
+// view nor unique enough to paginate on: several executions share a target, so
+// a slug cursor could skip or repeat rows.
+func (s *Server) ListExecutions(ctx context.Context, req gen.ListExecutionsRequestObject) (gen.ListExecutionsResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+
+	cursorTime, cursorID, err := parseExecutionCursor(req.Params.Cursor)
+	if err != nil {
+		return nil, err
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT e.entity_id, e.classification_id::text, e.signal_entity_id::text,
+		       e.target_entity_id, e.action, e.risk_class,
+		       e.approval_id::text, e.agent_id::text, e.skill_id::text,
+		       e.skill_version, e.status, e.result, e.duration_ms,
+		       e.verified, e.correlation_id, e.started_at, e.completed_at, e.created_at,
+		       te.slug
+		FROM executions e
+		JOIN entities te ON te.id = e.target_entity_id
+		WHERE ($1::text IS NULL OR e.status = $1)
+		  -- target accepts a slug or a uuid: the SPA passes an entity id,
+		  -- while a human poking the API reaches for the slug.
+		  AND ($2::text IS NULL OR te.slug = $2 OR e.target_entity_id::text = $2)
+		  -- the run tool encodes action as "run:{json}", so match the verb too
+		  AND ($3::text IS NULL OR e.action = $3 OR split_part(e.action, ':', 1) = $3)
+		  AND ($4::text IS NULL OR e.correlation_id = $4)
+		  AND ($5::timestamptz IS NULL
+		       OR (e.created_at, e.entity_id) < ($5::timestamptz, $6::uuid))
+		ORDER BY e.created_at DESC, e.entity_id DESC
+		LIMIT $7`,
+		req.Params.Status, req.Params.Target, req.Params.Action, req.Params.CorrelationId,
+		cursorTime, cursorID, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Execution{}
+	for rows.Next() {
+		var exec gen.Execution
+		var resultBytes []byte
+		var targetSlug string
+		if err := rows.Scan(&exec.Id, &exec.ClassificationId, &exec.SignalId,
+			&exec.Target, &exec.Action, &exec.RiskClass,
+			&exec.ApprovalId, &exec.AgentId, &exec.SkillId,
+			&exec.SkillVersion, &exec.Status, &resultBytes, &exec.DurationMs,
+			&exec.Verified, &exec.CorrelationId, &exec.StartedAt, &exec.CompletedAt,
+			&exec.CreatedAt, &targetSlug); err != nil {
+			return nil, err
+		}
+		var result map[string]any
+		if len(resultBytes) > 0 && json.Unmarshal(resultBytes, &result) == nil {
+			exec.Result = &result
+		}
+		// Target is stored as UUID, but we surface the slug
+		exec.Slug = targetSlug
+		items = append(items, exec)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	var next *string
+	if len(items) > limit {
+		items = items[:limit]
+		last := items[len(items)-1]
+		cursor := formatExecutionCursor(last.CreatedAt, last.Id)
+		next = &cursor
+	}
+	if items == nil {
+		items = []gen.Execution{}
+	}
+	return gen.ListExecutions200JSONResponse{Items: items, NextCursor: next}, nil
+}
+
+// Executions are ordered by (created_at DESC, entity_id DESC), so the cursor
+// has to carry both — created_at alone is not unique, and paginating on a
+// non-unique key drops or repeats rows at page boundaries.
+func formatExecutionCursor(createdAt time.Time, id uuid.UUID) string {
+	return createdAt.UTC().Format(time.RFC3339Nano) + "," + id.String()
+}
+
+func parseExecutionCursor(cursor *string) (*time.Time, *uuid.UUID, error) {
+	if cursor == nil || *cursor == "" {
+		return nil, nil, nil
+	}
+	rawTime, rawID, ok := strings.Cut(*cursor, ",")
+	if !ok {
+		return nil, nil, domain.ErrInvalidInput
+	}
+	t, err := time.Parse(time.RFC3339Nano, rawTime)
+	if err != nil {
+		return nil, nil, domain.ErrInvalidInput
+	}
+	id, err := uuid.Parse(rawID)
+	if err != nil {
+		return nil, nil, domain.ErrInvalidInput
+	}
+	return &t, &id, nil
+}
+
+func (s *Server) GetExecution(ctx context.Context, req gen.GetExecutionRequestObject) (gen.GetExecutionResponseObject, error) {
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	var exec gen.Execution
+	var resultBytes []byte
+	var targetSlug string
+	err = s.pool.QueryRow(ctx, `
+		SELECT e.entity_id, e.classification_id::text, e.signal_entity_id::text,
+		       e.target_entity_id, e.action, e.risk_class,
+		       e.approval_id::text, e.agent_id::text, e.skill_id::text,
+		       e.skill_version, e.status, e.result, e.duration_ms,
+		       e.verified, e.correlation_id, e.started_at, e.completed_at, e.created_at,
+		       te.slug
+		FROM executions e
+		JOIN entities te ON te.id = e.target_entity_id
+		WHERE e.entity_id = $1`, id).
+		Scan(&exec.Id, &exec.ClassificationId, &exec.SignalId,
+			&exec.Target, &exec.Action, &exec.RiskClass,
+			&exec.ApprovalId, &exec.AgentId, &exec.SkillId,
+			&exec.SkillVersion, &exec.Status, &resultBytes, &exec.DurationMs,
+			&exec.Verified, &exec.CorrelationId, &exec.StartedAt, &exec.CompletedAt,
+			&exec.CreatedAt, &targetSlug)
+	if err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: execution %s", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+	var result map[string]any
+	if len(resultBytes) > 0 && json.Unmarshal(resultBytes, &result) == nil {
+		exec.Result = &result
+	}
+	exec.Slug = targetSlug
+	return gen.GetExecution200JSONResponse(exec), nil
+}
+
+func (s *Server) RequestExecution(ctx context.Context, req gen.RequestExecutionRequestObject) (gen.RequestExecutionResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := uuid.NewV7()
+	if err != nil {
+		return nil, err
+	}
+
+	targetID, err := s.resolveEntityID(ctx, req.Body.Target)
+	if err != nil {
+		return nil, err
+	}
+
+	correlationID := uuid.New().String()
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	q := sqlcgen.New(tx)
+
+	// Full UUID, not a truncated prefix — an 8-char prefix of a UUIDv7
+	// collides for real under back-to-back requests since the leading bytes
+	// encode a millisecond timestamp (observed live via the MCP run tool).
+	execSlug := "exec:" + id.String()
+	if _, err := q.InsertEntity(ctx, sqlcgen.InsertEntityParams{
+		ID:         id,
+		Slug:       execSlug,
+		Type:       "execution",
+		Name:       req.Body.Action + " on " + req.Body.Target,
+		Attributes: []byte("{}"),
+	}); err != nil {
+		return nil, err
+	}
+
+	if err := q.InsertExecution(ctx, sqlcgen.InsertExecutionParams{
+		EntityID:       id,
+		TargetEntityID: &targetID,
+		Action:         req.Body.Action,
+		RiskClass:      "unclassified", // will be classified by classifier
+		CorrelationID:  correlationID,
+	}); err != nil {
+		return nil, err
+	}
+
+	// Re-read to get the full record.
+	var exec gen.Execution
+	var resultBytes []byte
+	var targetSlug string
+	err = tx.QueryRow(ctx, `
+		SELECT e.entity_id, e.classification_id::text, e.signal_entity_id::text,
+		       e.target_entity_id, e.action, e.risk_class,
+		       e.approval_id::text, e.agent_id::text, e.skill_id::text,
+		       e.skill_version, e.status, e.result, e.duration_ms,
+		       e.verified, e.correlation_id, e.started_at, e.completed_at, e.created_at,
+		       te.slug
+		FROM executions e
+		JOIN entities te ON te.id = e.target_entity_id
+		WHERE e.entity_id = $1`, id).
+		Scan(&exec.Id, &exec.ClassificationId, &exec.SignalId,
+			&exec.Target, &exec.Action, &exec.RiskClass,
+			&exec.ApprovalId, &exec.AgentId, &exec.SkillId,
+			&exec.SkillVersion, &exec.Status, &resultBytes, &exec.DurationMs,
+			&exec.Verified, &exec.CorrelationId, &exec.StartedAt, &exec.CompletedAt,
+			&exec.CreatedAt, &targetSlug)
+	if err != nil {
+		return nil, err
+	}
+	exec.Slug = targetSlug
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "create",
+		&id, "POST", "/api/v1/executions", "",
+		nil,
+		map[string]any{"action": req.Body.Action, "target": req.Body.Target}); auditErr != nil {
+		return nil, auditErr
+	}
+	if eventErr := observability.Event(ctx, q, "execution.requested", &id,
+		"info", "oikos-api", "",
+		map[string]any{"action": req.Body.Action, "target": req.Body.Target}); eventErr != nil {
+		return nil, eventErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.RequestExecution201JSONResponse(exec), nil
+}
+
+func (s *Server) CancelExecution(ctx context.Context, req gen.CancelExecutionRequestObject) (gen.CancelExecutionResponseObject, error) {
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	q := sqlcgen.New(tx)
+	if err := q.UpdateExecutionStatus(ctx, sqlcgen.UpdateExecutionStatusParams{
+		EntityID: id,
+		Status:   "cancelled",
+	}); err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: execution %s", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+
+	// Re-read.
+	var exec gen.Execution
+	var resultBytes []byte
+	var targetSlug string
+	err = tx.QueryRow(ctx, `
+		SELECT e.entity_id, e.classification_id::text, e.signal_entity_id::text,
+		       e.target_entity_id, e.action, e.risk_class,
+		       e.approval_id::text, e.agent_id::text, e.skill_id::text,
+		       e.skill_version, e.status, e.result, e.duration_ms,
+		       e.verified, e.correlation_id, e.started_at, e.completed_at, e.created_at,
+		       te.slug
+		FROM executions e
+		JOIN entities te ON te.id = e.target_entity_id
+		WHERE e.entity_id = $1`, id).
+		Scan(&exec.Id, &exec.ClassificationId, &exec.SignalId,
+			&exec.Target, &exec.Action, &exec.RiskClass,
+			&exec.ApprovalId, &exec.AgentId, &exec.SkillId,
+			&exec.SkillVersion, &exec.Status, &resultBytes, &exec.DurationMs,
+			&exec.Verified, &exec.CorrelationId, &exec.StartedAt, &exec.CompletedAt,
+			&exec.CreatedAt, &targetSlug)
+	if err != nil {
+		return nil, err
+	}
+	exec.Slug = targetSlug
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "cancel",
+		&id, "POST", "/api/v1/executions/"+req.Id+"/cancel", "",
+		nil,
+		map[string]any{"status": "cancelled"}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.CancelExecution200JSONResponse(exec), nil
+}

internal/httpapi/executions_cursor_test.go

@@ -0,0 +1,64 @@
+package httpapi
+
+import (
+	"testing"
+	"time"
+
+	"github.com/google/uuid"
+)
+
+// The cursor carries both created_at and entity_id because executions are
+// ordered by the pair. created_at alone is not unique — several executions can
+// share a millisecond — and paginating on a non-unique key silently drops or
+// repeats rows at page boundaries. The previous cursor was the target slug,
+// which is far less unique still: every execution against the same host shares
+// it.
+func TestExecutionCursorRoundTrips(t *testing.T) {
+	created := time.Date(2026, 7, 28, 9, 15, 30, 123456789, time.UTC)
+	id := uuid.MustParse("018f3a2b-0000-7000-8000-000000000042")
+
+	cursor := formatExecutionCursor(created, id)
+
+	gotTime, gotID, err := parseExecutionCursor(&cursor)
+	if err != nil {
+		t.Fatalf("parse: %v", err)
+	}
+	if !gotTime.Equal(created) {
+		t.Errorf("time round-trip: got %v, want %v", gotTime, created)
+	}
+	if *gotID != id {
+		t.Errorf("id round-trip: got %v, want %v", *gotID, id)
+	}
+}
+
+func TestExecutionCursorNanosecondsSurvive(t *testing.T) {
+	// Truncating to seconds would make the cursor ambiguous for executions
+	// started in the same second, which is the normal case for a plan whose
+	// steps run back to back.
+	a := time.Date(2026, 7, 28, 9, 15, 30, 1, time.UTC)
+	b := time.Date(2026, 7, 28, 9, 15, 30, 2, time.UTC)
+	id := uuid.New()
+
+	if formatExecutionCursor(a, id) == formatExecutionCursor(b, id) {
+		t.Error("cursors one nanosecond apart must not collide")
+	}
+}
+
+func TestExecutionCursorRejectsGarbage(t *testing.T) {
+	empty := ""
+	tm, id, err := parseExecutionCursor(&empty)
+	if err != nil || tm != nil || id != nil {
+		t.Errorf("empty cursor should mean 'no cursor', got %v/%v/%v", tm, id, err)
+	}
+
+	if tm, id, err := parseExecutionCursor(nil); err != nil || tm != nil || id != nil {
+		t.Errorf("nil cursor should mean 'no cursor', got %v/%v/%v", tm, id, err)
+	}
+
+	for _, bad := range []string{"nonsense", "2026-07-28T09:15:30Z", "notatime,018f3a2b-0000-7000-8000-000000000042", "2026-07-28T09:15:30Z,notauuid"} {
+		b := bad
+		if _, _, err := parseExecutionCursor(&b); err == nil {
+			t.Errorf("cursor %q should have been rejected", bad)
+		}
+	}
+}

internal/httpapi/gen/api.gen.go

@@ -86,6 +86,14 @@ const (
 	CheckKindTcp        CheckKind = "tcp"
 )
 
+// Defines values for CheckLastHealth.
+const (
+	CheckLastHealthDegraded CheckLastHealth = "degraded"
+	CheckLastHealthDown     CheckLastHealth = "down"
+	CheckLastHealthHealthy  CheckLastHealth = "healthy"
+	CheckLastHealthUnknown  CheckLastHealth = "unknown"
+)
+
 // Defines values for CheckCreateKind.
 const (
 	CheckCreateKindCertExpiry CheckCreateKind = "cert-expiry"
@@ -273,10 +281,10 @@ const (
 
 // Defines values for TrendDirection.
 const (
-	Degrading TrendDirection = "degrading"
-	Improving TrendDirection = "improving"
-	Stable    TrendDirection = "stable"
-	Unknown   TrendDirection = "unknown"
+	TrendDirectionDegrading TrendDirection = "degrading"
+	TrendDirectionImproving TrendDirection = "improving"
+	TrendDirectionStable    TrendDirection = "stable"
+	TrendDirectionUnknown   TrendDirection = "unknown"
 )
 
 // Defines values for ListApprovalsParamsStatus.
@@ -462,7 +470,13 @@ type Check struct {
 	Id        openapi_types.UUID      `json:"id"`
 	IntervalS int                     `json:"interval_s"`
 	Kind      CheckKind               `json:"kind"`
-	Slug      string                  `json:"slug"`
+
+	// LastHealth This check's own most recent verdict. An entity's health is the worst of these across its enabled checks, so this is what explains *why* an entity is degraded. Null until the check first runs.
+	LastHealth *CheckLastHealth `json:"last_health"`
+
+	// LastRunAt When this check last executed. Null = never run.
+	LastRunAt *time.Time `json:"last_run_at"`
+	Slug      string     `json:"slug"`
 
 	// Target Entity slug (instance-scoped)
 	Target *string `json:"target"`
@@ -477,6 +491,9 @@ type Check struct {
 // CheckKind defines model for Check.Kind.
 type CheckKind string
 
+// CheckLastHealth This check's own most recent verdict. An entity's health is the worst of these across its enabled checks, so this is what explains *why* an entity is degraded. Null until the check first runs.
+type CheckLastHealth string
+
 // CheckCreate defines model for CheckCreate.
 type CheckCreate struct {
 	Config     *map[string]interface{} `json:"config,omitempty"`
@@ -8208,175 +8225,177 @@ func (sh *strictHandler) GetTrends(w http.ResponseWriter, r *http.Request, entit
 // Base64 encoded, gzipped, json marshaled Swagger object
 var swaggerSpec = []string{
 
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+	"LrhQq++5Sg6fP37+/wEAAP//VvsxiT/wAAA=",
 }
 
 // GetSwagger returns the content of the embedded swagger specification file

internal/httpapi/helpers.go

@@ -0,0 +1,32 @@
+package httpapi
+
+import (
+	"crypto/sha256"
+	"encoding/hex"
+	"fmt"
+)
+
+// ─── Helpers ───────────────────────────────────────────────────────────
+
+func coalesceStr(s *string, def string) string {
+	if s == nil || *s == "" {
+		return def
+	}
+	return *s
+}
+
+func parseIntOrZero(s string) (int, error) {
+	var n int
+	for _, c := range s {
+		if c < '0' || c > '9' {
+			return 0, fmt.Errorf("invalid integer: %q", s)
+		}
+		n = n*10 + int(c-'0')
+	}
+	return n, nil
+}
+
+func hashToken(token string) string {
+	h := sha256.Sum256([]byte(token))
+	return hex.EncodeToString(h[:])
+}

internal/httpapi/impl.go

@@ -5,6 +5,7 @@ import (
 	"crypto/rand"
 	"crypto/sha256"
 	"encoding/json"
+	"errors"
 	"fmt"
 	"math/big"
 	"strconv"
@@ -24,7 +25,12 @@ import (
 const (
 	defaultLimit = 50
 	maxLimit     = 200
-	graphNodeCap = 500
+	// graphNodeCap bounds the whole-graph view. The cognition transactional
+	// types (execution, task) are audit records, not topology, and previously
+	// crowded out every host/lxc/service; the default whole-graph view below
+	// excludes them so the cap is spent on the actual fleet graph. Operators
+	// still reach executions/tasks via list_entities.
+	graphNodeCap = 2000
 )
 
 // actorInfo returns the caller's (type, label) from the request context,
@@ -60,19 +66,17 @@ func clampLimit(l *int) int {
 // resolveEntityID resolves a UUID-or-slug path/query value to the entity UUID.
 func (s *Server) resolveEntityID(ctx context.Context, idOrSlug string) (uuid.UUID, error) {
 	if id, err := uuid.Parse(idOrSlug); err == nil {
-		var found uuid.UUID
-		err := s.pool.QueryRow(ctx, "SELECT id FROM entities WHERE id = $1", id).Scan(&found)
-		if err == pgx.ErrNoRows {
+		entity, err := sqlcgen.New(s.pool).GetEntityByID(ctx, id)
+		if err != nil {
 			return uuid.Nil, fmt.Errorf("%w: %s", domain.ErrNotFound, idOrSlug)
 		}
-		return found, err
+		return entity.ID, nil
 	}
-	var id uuid.UUID
-	err := s.pool.QueryRow(ctx, "SELECT id FROM entities WHERE slug = $1", idOrSlug).Scan(&id)
-	if err == pgx.ErrNoRows {
+	entity, err := sqlcgen.New(s.pool).GetEntityBySlug(ctx, idOrSlug)
+	if err != nil {
 		return uuid.Nil, fmt.Errorf("%w: %s", domain.ErrNotFound, idOrSlug)
 	}
-	return id, err
+	return entity.ID, nil
 }
 
 // entityCols requires the entities table to be aliased as `e`, with
@@ -188,46 +192,37 @@ func (s *Server) GetEntityRelations(ctx context.Context, req gen.GetEntityRelati
 	if req.Params.Direction != nil {
 		dir = string(*req.Params.Direction)
 	}
-	rows, err := s.pool.Query(ctx, `
-		SELECT se.slug, te.slug, r.type, r.attributes, r.valid_from, r.valid_to
-		FROM relationships r
-		JOIN entities se ON se.id = r.source_id
-		JOIN entities te ON te.id = r.target_id
-		WHERE r.valid_to IS NULL
-		  AND (($3 IN ('out','both') AND r.source_id = $1)
-		    OR ($3 IN ('in','both')  AND r.target_id = $1))
-		  AND ($2::text IS NULL OR r.type = $2)
-		ORDER BY r.type, se.slug, te.slug`,
-		id, req.Params.RelType, dir)
+	relType := req.Params.RelType
+	rows, err := sqlcgen.New(s.pool).ListEntityRelations(ctx, sqlcgen.ListEntityRelationsParams{
+		Direction: dir,
+		ID:        id,
+		RelType:   relType,
+	})
 	if err != nil {
 		return nil, err
 	}
-	items, err := scanRelationships(rows)
-	if err != nil {
-		return nil, err
+	items := []gen.Relationship{}
+	for _, r := range rows {
+		var attrs *map[string]any
+		if len(r.Attributes) > 0 {
+			var m map[string]any
+			if json.Unmarshal(r.Attributes, &m) == nil && len(m) > 0 {
+				attrs = &m
+			}
+		}
+		validTo := r.ValidTo
+		items = append(items, gen.Relationship{
+			Source:     r.SourceSlug,
+			Target:     r.TargetSlug,
+			Type:       r.Type,
+			Attributes: attrs,
+			ValidFrom:  r.ValidFrom,
+			ValidTo:    validTo,
+		})
 	}
 	return gen.GetEntityRelations200JSONResponse{Items: items}, nil
 }
 
-func scanRelationships(rows pgx.Rows) ([]gen.Relationship, error) {
-	defer rows.Close()
-	items := []gen.Relationship{}
-	for rows.Next() {
-		var rel gen.Relationship
-		var attrsJSON []byte
-		if err := rows.Scan(&rel.Source, &rel.Target, &rel.Type,
-			&attrsJSON, &rel.ValidFrom, &rel.ValidTo); err != nil {
-			return nil, err
-		}
-		var attrs map[string]any
-		if len(attrsJSON) > 0 && json.Unmarshal(attrsJSON, &attrs) == nil && len(attrs) > 0 {
-			rel.Attributes = &attrs
-		}
-		items = append(items, rel)
-	}
-	return items, rows.Err()
-}
-
 func (s *Server) GetBlastRadius(ctx context.Context, req gen.GetBlastRadiusRequestObject) (gen.GetBlastRadiusResponseObject, error) {
 	id, err := s.resolveEntityID(ctx, req.Id)
 	if err != nil {
@@ -293,6 +288,15 @@ func (s *Server) GetGraph(ctx context.Context, req gen.GetGraphRequestObject) (g
 	var err error
 	truncated := false
 
+	// pgx can't infer the array element type from a nil *[]string (the
+	// param is absent from the request, not an empty list), so dereference
+	// to a plain []string first — nil there still encodes as SQL NULL, but
+	// pgx has a concrete type to work with.
+	var relTypes []string
+	if req.Params.RelType != nil {
+		relTypes = *req.Params.RelType
+	}
+
 	if req.Params.Root != nil && *req.Params.Root != "" {
 		rootID, rerr := s.resolveEntityID(ctx, *req.Params.Root)
 		if rerr != nil {
@@ -302,21 +306,26 @@ func (s *Server) GetGraph(ctx context.Context, req gen.GetGraphRequestObject) (g
 			SELECT `+entityCols+`
 			FROM blast_radius($1, $2, $3) b JOIN entities e ON e.id = b.entity_id
 			LEFT JOIN entity_status st ON st.entity_id = e.id
-			ORDER BY e.slug`, rootID, depth, req.Params.RelType)
+			ORDER BY e.slug`, rootID, depth, relTypes)
 	} else {
 		// Whole-graph view: pick the most-connected entities first so the
 		// graph shows actual topology, not just whatever sorts first
 		// alphabetically.  Without this the cap fills with exec:* rows and
 		// drops every host/lxc/service/vm — and every edge those entities
 		// connect — because edges require both endpoints in the node set.
+		// Exclude the cognition transactional types (execution/task): they
+		// are audit records rather than topology, and at ~380 rows they
+		// consumed most of the old 500-node cap.
 		nodes, err = s.queryEntities(ctx, `
 			SELECT `+entityCols+`
 			FROM entities e
 			LEFT JOIN entity_status st ON st.entity_id = e.id
-			WHERE e.id IN (
+			WHERE e.type NOT IN ('execution','task')
+			  AND e.id IN (
 				SELECT e2.id FROM entities e2
 				LEFT JOIN relationships r ON r.valid_to IS NULL
 					AND (r.source_id = e2.id OR r.target_id = e2.id)
+				WHERE e2.type NOT IN ('execution','task')
 				GROUP BY e2.id
 				ORDER BY count(r.type) DESC, e2.slug
 				LIMIT $1
@@ -336,21 +345,31 @@ func (s *Server) GetGraph(ctx context.Context, req gen.GetGraphRequestObject) (g
 	for i, n := range nodes {
 		ids[i] = uuid.UUID(n.Id)
 	}
-	rows, err := s.pool.Query(ctx, `
-		SELECT se.slug, te.slug, r.type, r.attributes, r.valid_from, r.valid_to
-		FROM relationships r
-		JOIN entities se ON se.id = r.source_id
-		JOIN entities te ON te.id = r.target_id
-		WHERE r.valid_to IS NULL
-		  AND r.source_id = ANY($1) AND r.target_id = ANY($1)
-		  AND ($2::text[] IS NULL OR r.type = ANY($2))
-		ORDER BY r.type, se.slug, te.slug`, ids, req.Params.RelType)
+	edgeRows, err := sqlcgen.New(s.pool).ListGraphEdges(ctx, sqlcgen.ListGraphEdgesParams{
+		Ids:      ids,
+		RelTypes: relTypes,
+	})
 	if err != nil {
 		return nil, err
 	}
-	edges, err := scanRelationships(rows)
-	if err != nil {
-		return nil, err
+	edges := []gen.Relationship{}
+	for _, r := range edgeRows {
+		var attrs *map[string]any
+		if len(r.Attributes) > 0 {
+			var m map[string]any
+			if json.Unmarshal(r.Attributes, &m) == nil && len(m) > 0 {
+				attrs = &m
+			}
+		}
+		validTo := r.ValidTo
+		edges = append(edges, gen.Relationship{
+			Source:     r.SourceSlug,
+			Target:     r.TargetSlug,
+			Type:       r.Type,
+			Attributes: attrs,
+			ValidFrom:  r.ValidFrom,
+			ValidTo:    validTo,
+		})
 	}
 
 	resp := gen.GetGraph200JSONResponse{Nodes: nodes, Edges: edges}
@@ -421,78 +440,70 @@ func (s *Server) GetOntology(ctx context.Context, req gen.GetOntologyRequestObje
 		Lifecycles:        []gen.LifecycleDef{},
 	}
 
-	rows, err := s.pool.Query(ctx, `
-		SELECT name, parent_type, is_abstract, domain, layer, description,
-		       lifecycle_id, attribute_schema, schema_version, status
-		FROM entity_types ORDER BY name`)
+	q := sqlcgen.New(s.pool)
+
+	etRows, err := q.ListEntityTypes(ctx)
 	if err != nil {
 		return nil, err
 	}
-	for rows.Next() {
-		var et gen.EntityType
-		var schemaVersion int
-		var schemaJSON []byte
-		if err := rows.Scan(&et.Name, &et.ParentType, &et.IsAbstract, &et.Domain,
-			&et.Layer, &et.Description, &et.LifecycleId, &schemaJSON,
-			&schemaVersion, &et.Status); err != nil {
-			rows.Close()
-			return nil, err
+	for _, et := range etRows {
+		schemaVersion := int(et.SchemaVersion)
+		var schema *map[string]any
+		if len(et.AttributeSchema) > 0 {
+			var s map[string]any
+			if json.Unmarshal(et.AttributeSchema, &s) == nil && s != nil {
+				schema = &s
+			}
 		}
-		et.SchemaVersion = &schemaVersion
-		var schema map[string]any
-		if len(schemaJSON) > 0 && json.Unmarshal(schemaJSON, &schema) == nil && schema != nil {
-			et.AttributeSchema = &schema
-		}
-		resp.EntityTypes = append(resp.EntityTypes, et)
-	}
-	rows.Close()
-	if rows.Err() != nil {
-		return nil, rows.Err()
+		resp.EntityTypes = append(resp.EntityTypes, gen.EntityType{
+			Name:            et.Name,
+			ParentType:      et.ParentType,
+			IsAbstract:      et.IsAbstract,
+			Domain:          et.Domain,
+			Layer:           gen.EntityTypeLayer(et.Layer),
+			Description:     et.Description,
+			LifecycleId:     et.LifecycleID,
+			SchemaVersion:   &schemaVersion,
+			AttributeSchema: schema,
+			Status:          gen.EntityTypeStatus(et.Status),
+		})
 	}
 
-	rows, err = s.pool.Query(ctx, `
-		SELECT name, inverse, source_type, target_type, cardinality, description
-		FROM relationship_types ORDER BY name`)
+	rtRows, err := q.ListRelationshipTypes(ctx)
 	if err != nil {
 		return nil, err
 	}
-	for rows.Next() {
-		var rt gen.RelationshipType
-		if err := rows.Scan(&rt.Name, &rt.Inverse, &rt.SourceType, &rt.TargetType,
-			&rt.Cardinality, &rt.Description); err != nil {
-			rows.Close()
-			return nil, err
-		}
-		resp.RelationshipTypes = append(resp.RelationshipTypes, rt)
-	}
-	rows.Close()
-	if rows.Err() != nil {
-		return nil, rows.Err()
+	for _, rt := range rtRows {
+		resp.RelationshipTypes = append(resp.RelationshipTypes, gen.RelationshipType{
+			Name:        rt.Name,
+			Inverse:     rt.Inverse,
+			SourceType:  rt.SourceType,
+			TargetType:  rt.TargetType,
+			Cardinality: gen.RelationshipTypeCardinality(rt.Cardinality),
+			Description: rt.Description,
+		})
 	}
 
-	rows, err = s.pool.Query(ctx, `
-		SELECT id, states, default_state, terminal_states, transitions
-		FROM lifecycle_defs ORDER BY id`)
+	lcRows, err := q.ListLifecycleDefs(ctx)
 	if err != nil {
 		return nil, err
 	}
-	for rows.Next() {
-		var lc gen.LifecycleDef
-		var terminal []string
-		var transJSON []byte
-		if err := rows.Scan(&lc.Id, &lc.States, &lc.DefaultState, &terminal, &transJSON); err != nil {
-			rows.Close()
-			return nil, err
+	for _, lc := range lcRows {
+		terminal := lc.TerminalStates
+		var transitions map[string]any
+		if err := json.Unmarshal(lc.Transitions, &transitions); err != nil {
+			return nil, fmt.Errorf("lifecycle %s transitions: %w", lc.ID, err)
 		}
-		lc.TerminalStates = &terminal
-		if err := json.Unmarshal(transJSON, &lc.Transitions); err != nil {
-			rows.Close()
-			return nil, fmt.Errorf("lifecycle %s transitions: %w", lc.Id, err)
-		}
-		resp.Lifecycles = append(resp.Lifecycles, lc)
+		resp.Lifecycles = append(resp.Lifecycles, gen.LifecycleDef{
+			Id:             lc.ID,
+			States:         lc.States,
+			DefaultState:   lc.DefaultState,
+			TerminalStates: &terminal,
+			Transitions:    transitions,
+		})
 	}
-	rows.Close()
-	return resp, rows.Err()
+
+	return resp, nil
 }
 
 // ─── Signals ──────────────────────────────────────────────────────────
@@ -807,7 +818,7 @@ func (s *Server) QueryAudit(ctx context.Context, req gen.QueryAuditRequestObject
 
 	rows, err := s.pool.Query(ctx, `
 		SELECT id, ts, actor_type, actor_id::text, action, entity_id::text,
-		       method, path, status_code, detail, source_ip, correlation_id
+		       method, path, status_code, detail, source_ip, correlation_id, session_id::text
 		FROM audit_log
 		WHERE ($1::text IS NULL OR actor_type = $1)
 		  AND ($2::text IS NULL OR actor_id::text = $2)
@@ -828,10 +839,10 @@ func (s *Server) QueryAudit(ctx context.Context, req gen.QueryAuditRequestObject
 	for rows.Next() {
 		var a gen.AuditEntry
 		var detailBytes []byte
-		var actID, entID, method, path, sourceIP, corrID *string
+		var actID, entID, method, path, sourceIP, corrID, sessionID *string
 		var statusCode *int
 		if err := rows.Scan(&a.Id, &a.Ts, &a.ActorType, &actID, &a.Action, &entID,
-			&method, &path, &statusCode, &detailBytes, &sourceIP, &corrID); err != nil {
+			&method, &path, &statusCode, &detailBytes, &sourceIP, &corrID, &sessionID); err != nil {
 			return nil, err
 		}
 		a.ActorId = actID
@@ -989,6 +1000,7 @@ func (s *Server) CreateEntity(ctx context.Context, req gen.CreateEntityRequestOb
 	entityID := inserted.ID
 	if auditErr := observability.Audit(ctx, q, actorType, actor, "create",
 		&entityID, "POST", "/api/v1/entities", "",
+		nil,
 		map[string]any{"type": req.Body.Type, "slug": slug}); auditErr != nil {
 		return nil, auditErr
 	}
@@ -999,7 +1011,9 @@ func (s *Server) CreateEntity(ctx context.Context, req gen.CreateEntityRequestOb
 		return nil, eventErr
 	}
 
-	ensureDefaultChecks(ctx, tx, inserted.ID, slug, req.Body.Type, attrsJSON)
+	if err := ensureDefaultChecks(ctx, tx, inserted.ID, slug, req.Body.Type, inserted.Name, attrsJSON); err != nil {
+		return nil, err
+	}
 
 	if err := tx.Commit(ctx); err != nil {
 		return nil, err
@@ -1050,49 +1064,15 @@ func (s *Server) PatchEntity(ctx context.Context, req gen.PatchEntityRequestObje
 
 	// Validate lifecycle transition if state is being changed.
 	if req.Body.State != nil && *req.Body.State != "" {
-		// Get lifecycle def for the entity's type.
-		lc, err := sqlcgen.New(tx).GetLifecycleForType(ctx, current.Type)
-		if err != nil {
-			if err == pgx.ErrNoRows {
-				// No lifecycle defined — any state is allowed.
-			} else {
-				return nil, err
-			}
-		} else {
-			var transitions map[string]map[string]json.RawMessage
-			if err := json.Unmarshal(lc.Transitions, &transitions); err != nil {
-				return nil, fmt.Errorf("parse lifecycle transitions: %w", err)
-			}
-
-			fromState := ""
-			if current.State != nil {
-				fromState = *current.State
-			}
-			toState := *req.Body.State
-
-			if toState != fromState {
-				tos, ok := transitions[fromState]
-				if !ok {
-					return nil, fmt.Errorf("%w: no transitions from %q", domain.ErrInvalidTransition, fromState)
-				}
-				trans, ok := tos[toState]
-				if !ok {
-					return nil, fmt.Errorf("%w: %s → %s", domain.ErrInvalidTransition, fromState, toState)
-				}
-
-				// Parse preconditions: {"requires": ["check-name", ...]}
-				var gate struct {
-					Requires []string `json:"requires"`
-				}
-				if err := json.Unmarshal(trans, &gate); err == nil && len(gate.Requires) > 0 {
-					for _, check := range gate.Requires {
-						if err := checkPrecondition(ctx, tx, id, current.Type, check); err != nil {
-							return nil, fmt.Errorf("%w: precondition %q not met: %v",
-								domain.ErrInvalidTransition, check, err)
-						}
-					}
-				}
+		fromState := ""
+		if current.State != nil {
+			fromState = *current.State
+		}
+		if err := db.ValidateTransition(ctx, tx, id, current.Type, fromState, *req.Body.State); err != nil {
+			if errors.Is(err, db.ErrTransitionInvalid) {
+				return nil, fmt.Errorf("%w: %v", domain.ErrInvalidTransition, err)
 			}
+			return nil, err
 		}
 	}
 
@@ -1131,6 +1111,7 @@ func (s *Server) PatchEntity(ctx context.Context, req gen.PatchEntityRequestObje
 	patchActorType, patchActor := actorInfo(ctx)
 	if auditErr := observability.Audit(ctx, q, patchActorType, patchActor, "patch",
 		&id, "PATCH", "/api/v1/entities/"+req.Id, "",
+		nil,
 		map[string]any{"version": expectedVersion}); auditErr != nil {
 		return nil, auditErr
 	}
@@ -1260,12 +1241,15 @@ func (s *Server) EnrollClient(ctx context.Context, req gen.EnrollClientRequestOb
 	entityID := id
 	_ = observability.Audit(ctx, q, "operator", actor, "enroll",
 		&entityID, "POST", "/api/v1/clients/enroll", "",
+		nil,
 		map[string]any{"slug": req.Body.Slug, "mesh_ip": meshIP})
 	_ = observability.Event(ctx, q, "client.enrolled", &entityID,
 		"info", "oikos-api", "",
 		map[string]any{"slug": req.Body.Slug, "type": current.Type})
 
-	ensureDefaultChecks(ctx, tx, id, req.Body.Slug, current.Type, attrsJSON)
+	if err := ensureDefaultChecks(ctx, tx, id, req.Body.Slug, current.Type, current.Name, attrsJSON); err != nil {
+		return nil, err
+	}
 
 	if err := tx.Commit(ctx); err != nil {
 		return nil, err
@@ -1452,6 +1436,7 @@ func (s *Server) ProvisionEntity(ctx context.Context, req gen.ProvisionEntityReq
 	_, actor := actorInfo(ctx)
 	_ = observability.Audit(ctx, q, "operator", actor, "provision",
 		&entityID, "POST", "/api/v1/entities/provision", "",
+		nil,
 		map[string]any{"slug": req.Body.Slug, "host": hostSlug})
 	_ = observability.Event(ctx, q, "entity.provisioned", &entityID,
 		"info", "oikos-api", "",
@@ -1542,98 +1527,5 @@ func generateAgeKeypair() (pubKey, privKey string, err error) {
 	return pub, priv, nil
 }
 
-// checkPrecondition validates a named lifecycle transition precondition.
-func checkPrecondition(ctx context.Context, tx pgx.Tx, entityID uuid.UUID, entityType, check string) error {
-	switch check {
-	case "no-inbound-edges":
-		var count int
-		err := tx.QueryRow(ctx,
-			"SELECT count(*) FROM relationships WHERE target_id = $1 AND valid_to IS NULL", entityID).Scan(&count)
-		if err != nil {
-			return err
-		}
-		if count > 0 {
-			return fmt.Errorf("%d inbound relationship edges remaining", count)
-		}
-	case "backups-verified":
-		var attrs string
-		err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs)
-		if err != nil {
-			return err
-		}
-		if !strings.Contains(attrs, "backups_verified") {
-			return fmt.Errorf("backup verification not recorded in entity attributes")
-		}
-	case "secrets-revoked":
-		var attrs string
-		err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs)
-		if err != nil {
-			return err
-		}
-		if !strings.Contains(attrs, "secrets_revoked") {
-			return fmt.Errorf("secret revocation not recorded in entity attributes")
-		}
-	case "ingress-dns-removed":
-		var attrs string
-		err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs)
-		if err != nil {
-			return err
-		}
-		if !strings.Contains(attrs, "ingress_dns_removed") {
-			return fmt.Errorf("ingress/DNS removal not recorded in entity attributes")
-		}
-	case "age-key-enrolled-if-needed":
-		if entityType == "workstation" {
-			var attrs string
-			err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs)
-			if err != nil {
-				return err
-			}
-			if !strings.Contains(attrs, "age_pubkey") {
-				return fmt.Errorf("age key not enrolled (no age_pubkey in attributes)")
-			}
-		}
-	case "mesh-joined-if-needed":
-		if entityType == "workstation" {
-			var attrs string
-			err := tx.QueryRow(ctx, "SELECT coalesce(attributes::text,'{}') FROM entities WHERE id = $1", entityID).Scan(&attrs)
-			if err != nil {
-				return err
-			}
-			if !strings.Contains(attrs, "mesh_ip") {
-				return fmt.Errorf("mesh not joined (no mesh_ip in attributes)")
-			}
-		}
-	case "health-check-answering":
-		var health string
-		err := tx.QueryRow(ctx, "SELECT health FROM entity_status WHERE entity_id = $1", entityID).Scan(&health)
-		if err != nil || health == "unknown" || health == "down" {
-			return fmt.Errorf("health check not answering (status: %s)", health)
-		}
-	case "doc-page-complete":
-		var count int
-		err := tx.QueryRow(ctx, `
-			SELECT count(*) FROM relationships r
-			JOIN entities ke ON ke.id = r.source_id
-			WHERE r.target_id = $1 AND r.valid_to IS NULL
-			  AND r.type = 'documents' AND ke.type IN ('document','runbook','investigation')`,
-			entityID).Scan(&count)
-		if err != nil {
-			return err
-		}
-		if count == 0 {
-			return fmt.Errorf("no documentation linked to entity")
-		}
-	case "inventory-entry", "ip-reserved", "storage-pool-chosen", "cancelled-note",
-		"preflight-passed", "error-summary", "replacement-live-or-role-retired",
-		"replacement-failed", "post-verify-passed", "recovery-verified", "written-off",
-		"ingress-live-if-public", "doc-page-stub":
-		// Soft checks — always pass. These are operator-confirmed via the
-		// transition request itself, or are not mechanically enforceable.
-	default:
-		// Unknown preconditions are skipped (operator intent overrides).
-	}
-	return nil
-}
 
 // ─── Helpers ───────────────────────────────────────────────────────────

internal/httpapi/knowledge.go

@@ -50,6 +50,7 @@ func (s *Server) serveRecentKnowledge(w http.ResponseWriter, req *http.Request)
 		FROM knowledge_entities ke
 		JOIN entities e ON e.id = ke.entity_id
 		WHERE ($1 = '' OR ke.source = $1)
+		  AND ke.deleted_at IS NULL
 		ORDER BY ke.updated_at DESC
 		LIMIT $2`, source, limit)
 	if err != nil {
@@ -82,6 +83,7 @@ func (s *Server) serveRecentKnowledge(w http.ResponseWriter, req *http.Request)
 		       COUNT(*) FILTER (WHERE ke.source = 'nomos-agent'),
 		       COUNT(*) FILTER (WHERE ke.updated_at > now() - interval '7 days')
 		FROM knowledge_entities ke JOIN entities e ON e.id = ke.entity_id
+		WHERE ke.deleted_at IS NULL
 		GROUP BY e.type`)
 	if err == nil {
 		defer srows.Close()
@@ -128,15 +130,19 @@ func (s *Server) serveKnowledgeContent(w http.ResponseWriter, req *http.Request)
 		return
 	}
 
-	var title, content, source string
+	var title, content, source, editedBy string
 	var tags []string
 	var updatedAt string
+	var revisions int
 	err = s.pool.QueryRow(ctx, `
-		SELECT ke.title, ke.content, COALESCE(ke.source,''), ke.tags, ke.updated_at::text
+		SELECT ke.title, ke.content, COALESCE(ke.source,''), COALESCE(ke.edited_by,''),
+		       ke.tags, ke.updated_at::text,
+		       (SELECT count(*) FROM knowledge_revisions kr WHERE kr.entity_id = ke.entity_id)
 		FROM knowledge_entities ke
 		JOIN entities e ON e.id = ke.entity_id
-		WHERE e.slug = $1 OR e.id::text = $1`, idOrSlug).
-		Scan(&title, &content, &source, &tags, &updatedAt)
+		WHERE (e.slug = $1 OR e.id::text = $1)
+		  AND ke.deleted_at IS NULL`, idOrSlug).
+		Scan(&title, &content, &source, &editedBy, &tags, &updatedAt, &revisions)
 	if err != nil {
 		writeProblem(w, req, http.StatusNotFound, "no knowledge content for entity", "")
 		return
@@ -150,8 +156,10 @@ func (s *Server) serveKnowledgeContent(w http.ResponseWriter, req *http.Request)
 		"title":      title,
 		"content":    content,
 		"source":     source,
+		"edited_by":  editedBy,
 		"tags":       tags,
 		"updated_at": updatedAt,
+		"revisions":  revisions,
 	})
 }
 
@@ -169,6 +177,7 @@ func (s *Server) SearchKnowledge(ctx context.Context, request gen.SearchKnowledg
 		JOIN entities e ON e.id = ke.entity_id
 		JOIN entity_types et ON et.name = e.type
 		WHERE ke.search @@ plainto_tsquery('english', $1)
+		  AND ke.deleted_at IS NULL
 		ORDER BY rank DESC
 		LIMIT $2`,
 		q, limit)
@@ -232,6 +241,7 @@ func (s *Server) GetEntityKnowledge(ctx context.Context, request gen.GetEntityKn
 		WHERE target.slug = $1
 		  AND r.valid_to IS NULL
 		  AND r.type IN ('documents', 'about')
+		  AND ke.deleted_at IS NULL
 		UNION
 		SELECT e.id, e.slug, COALESCE(et.name,''), ke.title, ke.source, ke.tags
 		FROM knowledge_entities ke
@@ -242,6 +252,7 @@ func (s *Server) GetEntityKnowledge(ctx context.Context, request gen.GetEntityKn
 		JOIN entities ent ON ent.type = target_type.name AND ent.slug = $1
 		WHERE r.valid_to IS NULL
 		  AND r.type = 'procedure-for'
+		  AND ke.deleted_at IS NULL
 		ORDER BY 2`,
 		entitySlug)
 	if err != nil {

internal/httpapi/knowledge_drift.go

@@ -0,0 +1,544 @@
+package httpapi
+
+import (
+	"encoding/json"
+	"fmt"
+	"log/slog"
+	"net/http"
+	"sort"
+	"strconv"
+	"strings"
+)
+
+// Drift tooling for the knowledge base — the maintenance half of the wiki.
+//
+// These endpoints exist because the knowledge base measurably rots on its
+// own. Two failure modes are already present in live data:
+//
+//   - **Duplicate pileup.** upsert_knowledge keys on exact title, so a note
+//     titled "rclone backup live inspection — 2026-07-15 10:08 UTC" and one
+//     titled "... 11:18 UTC" are different notes. A single day of agent
+//     activity produced eight near-identical investigations that should have
+//     been one living page. Nothing surfaced that, so it kept happening.
+//   - **Tag drift.** `oom` and `OOM` were separate tags; so were `422` and
+//     `proton-422`. Each split halves the usefulness of tag navigation, and
+//     neither is visible from any single note.
+//
+// normalizeTags (knowledge_write.go) stops new casing splits at the door;
+// these endpoints clean up what's already there and make the rot visible.
+
+// serveKnowledgeTags returns the tag index: every tag with its usage count,
+// plus the distinct casings actually stored. `variants` is the interesting
+// column — it's how the operator discovers that `oom` and `OOM` are the same
+// idea filed twice, which no individual note reveals.
+func (s *Server) serveKnowledgeTags(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT lower(tag) AS norm,
+		       count(*) AS uses,
+		       array_agg(DISTINCT tag ORDER BY tag) AS variants
+		FROM knowledge_entities ke, unnest(ke.tags) AS tag
+		WHERE ke.deleted_at IS NULL
+		GROUP BY lower(tag)
+		ORDER BY uses DESC, norm`)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	type tagRow struct {
+		Tag      string   `json:"tag"`
+		Uses     int      `json:"uses"`
+		Variants []string `json:"variants"`
+		// True when the same tag is stored under more than one casing —
+		// the UI badges these as needing a normalize.
+		Split bool `json:"split"`
+	}
+	items := []tagRow{}
+	for rows.Next() {
+		var t tagRow
+		if err := rows.Scan(&t.Tag, &t.Uses, &t.Variants); err != nil {
+			slog.Error("httpapi: knowledge/tags row scan failed", "error", err)
+			continue
+		}
+		t.Split = len(t.Variants) > 1
+		items = append(items, t)
+	}
+
+	writeJSON(w, map[string]any{"items": items})
+}
+
+// serveRenameKnowledgeTag rewrites one or more tags to a single target across
+// every live note — the merge/rename/normalize action behind the tag manager.
+// Passing several `from` values into one `to` is the merge case
+// (`{"from":["422","proton-422"],"to":"proton-422"}`); passing one is a plain
+// rename; passing the mixed-case variants is the normalize case.
+func (s *Server) serveRenameKnowledgeTag(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	var body struct {
+		From []string `json:"from"`
+		To   string   `json:"to"`
+	}
+	if err := json.NewDecoder(req.Body).Decode(&body); err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid request body", err.Error())
+		return
+	}
+	to := strings.ToLower(strings.TrimSpace(body.To))
+	from := []string{}
+	for _, f := range body.From {
+		if f = strings.TrimSpace(f); f != "" {
+			from = append(from, f)
+		}
+	}
+	if to == "" || len(from) == 0 {
+		writeProblem(w, req, http.StatusBadRequest, "from and to are required", "")
+		return
+	}
+
+	// Rebuild each affected note's tag array: map every `from` member to
+	// `to`, leave everything else alone, then de-duplicate. The dedupe
+	// matters for the merge case — a note tagged both `422` and
+	// `proton-422` would otherwise end up with `proton-422` twice.
+	//
+	// This is a plain UPDATE on knowledge_entities, so trg_knowledge_revision
+	// fires and every affected note gets a revision. A tag merge across 17
+	// notes is exactly the kind of bulk edit worth being able to inspect
+	// afterwards.
+	tag, err := s.pool.Exec(ctx, `
+		UPDATE knowledge_entities ke
+		SET tags = sub.new_tags, updated_at = now()
+		FROM (
+			SELECT k.entity_id,
+			       ARRAY(SELECT DISTINCT CASE WHEN lower(t) = ANY($1) THEN $2 ELSE t END
+			             FROM unnest(k.tags) AS t) AS new_tags
+			FROM knowledge_entities k
+			WHERE k.deleted_at IS NULL
+			  AND EXISTS (SELECT 1 FROM unnest(k.tags) AS t WHERE lower(t) = ANY($1))
+		) AS sub
+		WHERE ke.entity_id = sub.entity_id`,
+		lowerAll(from), to)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "rename failed", err.Error())
+		return
+	}
+
+	_, actorLabel := actorInfo(ctx)
+	slog.Info("knowledge tags renamed", "from", from, "to", to,
+		"notes", tag.RowsAffected(), "actor", actorLabel)
+	writeJSON(w, map[string]any{"ok": true, "notes_updated": tag.RowsAffected()})
+}
+
+// serveKnowledgeDuplicates clusters notes whose titles are near-identical.
+//
+// Pairwise trigram similarity is computed in SQL (indexed, and the whole
+// point of pulling in pg_trgm); the grouping is done here in Go. Returning
+// clusters rather than pairs matters for the real data: the rclone pileup
+// produces dozens of pairs, which is unreadable, versus one cluster, which
+// is the actionable unit.
+//
+// The grouping uses **complete linkage** — a note joins a cluster only if it
+// is similar to every member already in it. The obvious implementation
+// (union-find over the pairs) is single linkage, and on this data it chains
+// badly: "A~B, B~C" merged notes that were not remotely alike, collapsing
+// fifteen distinct backup events into one unusable blob. Requiring mutual
+// similarity keeps clusters tight enough to act on.
+//
+// Even so, these are *candidates for review*, never a verdict. The five
+// "Lifecycle: <verb> a node" runbooks are mutually similar by title and are
+// five deliberately distinct documents — no threshold distinguishes them
+// from a genuine duplicate, so merging stays a manual, previewed action.
+func (s *Server) serveKnowledgeDuplicates(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	// 0.6, tuned against the live data: at 0.45 the "Lifecycle: <verb> a
+	// node" runbooks (five deliberately distinct documents that happen to
+	// share a naming template) formed a false-positive cluster; 0.6 clears
+	// that down to a single borderline pair while keeping every genuine
+	// duplicate cluster (the rclone/apt-audit/uptime pileups) intact.
+	// Tunable per request — the UI exposes this as the review net widens.
+	threshold := 0.6
+	if t := req.URL.Query().Get("threshold"); t != "" {
+		if v, err := strconv.ParseFloat(t, 64); err == nil && v > 0 && v <= 1 {
+			threshold = v
+		}
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT a.slug, b.slug, similarity(ka.title, kb.title) AS sim
+		FROM knowledge_entities ka
+		JOIN knowledge_entities kb ON ka.entity_id < kb.entity_id
+		JOIN entities a ON a.id = ka.entity_id
+		JOIN entities b ON b.id = kb.entity_id
+		WHERE ka.deleted_at IS NULL AND kb.deleted_at IS NULL
+		  AND similarity(ka.title, kb.title) > $1
+		ORDER BY sim DESC`, threshold)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	type pair struct {
+		A, B string
+		Sim  float64
+	}
+	pairs := []pair{}
+	for rows.Next() {
+		var p pair
+		if err := rows.Scan(&p.A, &p.B, &p.Sim); err != nil {
+			slog.Error("httpapi: knowledge/duplicates row scan failed", "error", err)
+			continue
+		}
+		pairs = append(pairs, p)
+	}
+
+	// Complete-linkage grouping. `pairs` arrives sorted by similarity
+	// descending, so each new cluster is seeded from the strongest remaining
+	// pair and then only grows with notes that are similar to *everything*
+	// already inside it.
+	sim := make(map[string]float64, len(pairs)*2)
+	key := func(a, b string) string {
+		if a > b {
+			a, b = b, a
+		}
+		return a + "\x00" + b
+	}
+	for _, p := range pairs {
+		sim[key(p.A, p.B)] = p.Sim
+	}
+	linked := func(a, b string) bool { return sim[key(a, b)] > 0 }
+
+	assigned := map[string]bool{}
+	type rawCluster struct {
+		members []string
+		top     float64
+	}
+	raw := []rawCluster{}
+
+	for _, p := range pairs {
+		if assigned[p.A] || assigned[p.B] {
+			continue
+		}
+		c := rawCluster{members: []string{p.A, p.B}, top: p.Sim}
+		assigned[p.A], assigned[p.B] = true, true
+
+		// Sweep the remaining pairs for candidates that connect to every
+		// current member. Repeat until a full pass adds nothing, since
+		// admitting one member can qualify another.
+		for grew := true; grew; {
+			grew = false
+			for _, q := range pairs {
+				for _, cand := range []string{q.A, q.B} {
+					if assigned[cand] {
+						continue
+					}
+					ok := true
+					for _, m := range c.members {
+						if !linked(cand, m) {
+							ok = false
+							break
+						}
+					}
+					if ok {
+						c.members = append(c.members, cand)
+						assigned[cand] = true
+						grew = true
+					}
+				}
+			}
+		}
+		raw = append(raw, c)
+	}
+
+	groups := map[string][]string{}
+	best := map[string]float64{}
+	for _, c := range raw {
+		root := c.members[0]
+		groups[root] = c.members
+		best[root] = c.top
+	}
+
+	// Re-fetch display detail for the clustered slugs only.
+	type member struct {
+		Slug      string `json:"slug"`
+		Title     string `json:"title"`
+		Kind      string `json:"kind"`
+		Size      int    `json:"size"`
+		UpdatedAt string `json:"updated_at"`
+		EditedBy  string `json:"edited_by"`
+	}
+	detail := map[string]member{}
+	if len(groups) > 0 {
+		all := []string{}
+		for _, g := range groups {
+			all = append(all, g...)
+		}
+		drows, derr := s.pool.Query(ctx, `
+			SELECT e.slug, ke.title, e.type, length(ke.content),
+			       ke.updated_at::text, COALESCE(ke.edited_by,'')
+			FROM knowledge_entities ke
+			JOIN entities e ON e.id = ke.entity_id
+			WHERE e.slug = ANY($1) AND ke.deleted_at IS NULL`, all)
+		if derr != nil {
+			writeProblem(w, req, http.StatusInternalServerError, "detail query failed", derr.Error())
+			return
+		}
+		defer drows.Close()
+		for drows.Next() {
+			var m member
+			if err := drows.Scan(&m.Slug, &m.Title, &m.Kind, &m.Size, &m.UpdatedAt, &m.EditedBy); err != nil {
+				slog.Error("httpapi: knowledge/duplicates detail scan failed", "error", err)
+				continue
+			}
+			detail[m.Slug] = m
+		}
+	}
+
+	type cluster struct {
+		Members   []member `json:"members"`
+		TopSim    float64  `json:"top_similarity"`
+		TotalSize int      `json:"total_size"`
+	}
+	out := []cluster{}
+	for root, slugs := range groups {
+		c := cluster{TopSim: best[root]}
+		for _, sl := range slugs {
+			if m, ok := detail[sl]; ok {
+				c.Members = append(c.Members, m)
+				c.TotalSize += m.Size
+			}
+		}
+		if len(c.Members) < 2 {
+			continue
+		}
+		// Newest first inside a cluster — the most recent note is usually
+		// the one worth keeping as the merge target.
+		sort.Slice(c.Members, func(i, j int) bool {
+			return c.Members[i].UpdatedAt > c.Members[j].UpdatedAt
+		})
+		out = append(out, c)
+	}
+	// Biggest clusters first: an eight-note pileup deserves attention before
+	// a two-note coincidence.
+	sort.Slice(out, func(i, j int) bool {
+		if len(out[i].Members) != len(out[j].Members) {
+			return len(out[i].Members) > len(out[j].Members)
+		}
+		return out[i].TopSim > out[j].TopSim
+	})
+
+	writeJSON(w, map[string]any{"clusters": out, "threshold": threshold})
+}
+
+// serveKnowledgeOrphans surfaces notes that have fallen out of every
+// navigation path — the ones that are technically present but effectively
+// unreachable, and so quietly stop being maintained.
+//
+// Three independent reasons, reported per note (a note can have several):
+//   - untagged: invisible to tag navigation
+//   - unlinked: not `about` any entity, so it never appears on a machine's page
+//   - stale: untouched for 90+ days
+func (s *Server) serveKnowledgeOrphans(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	staleDays := 90
+	if d := req.URL.Query().Get("stale_days"); d != "" {
+		if v, err := strconv.Atoi(d); err == nil && v > 0 && v <= 3650 {
+			staleDays = v
+		}
+	}
+
+	rows, err := s.pool.Query(ctx, fmt.Sprintf(`
+		SELECT e.slug, ke.title, e.type, COALESCE(ke.edited_by,''),
+		       ke.updated_at::text,
+		       (ke.tags IS NULL OR cardinality(ke.tags) = 0) AS untagged,
+		       NOT EXISTS (
+		         SELECT 1 FROM relationships r
+		         WHERE r.source_id = ke.entity_id AND r.valid_to IS NULL
+		           AND r.type IN ('documents', 'about')
+		       ) AS unlinked,
+		       (ke.updated_at < now() - interval '%d days') AS stale
+		FROM knowledge_entities ke
+		JOIN entities e ON e.id = ke.entity_id
+		WHERE ke.deleted_at IS NULL
+		ORDER BY ke.updated_at ASC`, staleDays))
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	type orphan struct {
+		Slug      string   `json:"slug"`
+		Title     string   `json:"title"`
+		Kind      string   `json:"kind"`
+		EditedBy  string   `json:"edited_by"`
+		UpdatedAt string   `json:"updated_at"`
+		Reasons   []string `json:"reasons"`
+	}
+	items := []orphan{}
+	counts := map[string]int{"untagged": 0, "unlinked": 0, "stale": 0}
+	for rows.Next() {
+		var o orphan
+		var untagged, unlinked, stale bool
+		if err := rows.Scan(&o.Slug, &o.Title, &o.Kind, &o.EditedBy, &o.UpdatedAt,
+			&untagged, &unlinked, &stale); err != nil {
+			slog.Error("httpapi: knowledge/orphans row scan failed", "error", err)
+			continue
+		}
+		o.Reasons = []string{}
+		if untagged {
+			o.Reasons = append(o.Reasons, "untagged")
+			counts["untagged"]++
+		}
+		if unlinked {
+			o.Reasons = append(o.Reasons, "unlinked")
+			counts["unlinked"]++
+		}
+		if stale {
+			o.Reasons = append(o.Reasons, "stale")
+			counts["stale"]++
+		}
+		if len(o.Reasons) > 0 {
+			items = append(items, o)
+		}
+	}
+
+	writeJSON(w, map[string]any{
+		"items":      items,
+		"counts":     counts,
+		"stale_days": staleDays,
+	})
+}
+
+// serveMergeKnowledge folds several notes into one: each source's body is
+// appended to the target under a provenance heading, the union of all tags is
+// kept, and the sources are soft-deleted.
+//
+// Append rather than discard, and soft-delete rather than hard: a merge is a
+// judgement call made from a similarity score, and the operator needs to be
+// able to walk it back. The target's pre-merge state is captured by the
+// revision trigger, so the merge itself is undoable from the History tab.
+func (s *Server) serveMergeKnowledge(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	var body struct {
+		Target  string   `json:"target"`
+		Sources []string `json:"sources"`
+	}
+	if err := json.NewDecoder(req.Body).Decode(&body); err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid request body", err.Error())
+		return
+	}
+	if strings.TrimSpace(body.Target) == "" || len(body.Sources) == 0 {
+		writeProblem(w, req, http.StatusBadRequest, "target and sources are required", "")
+		return
+	}
+
+	targetID, err := s.resolveKnowledgeEntity(ctx, body.Target)
+	if err != nil {
+		writeProblem(w, req, http.StatusNotFound, "target note not found", body.Target)
+		return
+	}
+	_, actorLabel := actorInfo(ctx)
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "begin failed", err.Error())
+		return
+	}
+	defer tx.Rollback(ctx)
+
+	var merged []string
+	var appended strings.Builder
+	tagSet := map[string]bool{}
+
+	for _, srcSlug := range body.Sources {
+		if srcSlug == body.Target {
+			continue // merging a note into itself would duplicate its body
+		}
+		var srcTitle, srcContent, srcUpdated string
+		var srcTags []string
+		err := tx.QueryRow(ctx, `
+			SELECT ke.title, ke.content, COALESCE(ke.tags,'{}'), ke.updated_at::text
+			FROM knowledge_entities ke
+			JOIN entities e ON e.id = ke.entity_id
+			WHERE (e.slug = $1 OR e.id::text = $1) AND ke.deleted_at IS NULL`,
+			srcSlug).Scan(&srcTitle, &srcContent, &srcTags, &srcUpdated)
+		if err != nil {
+			slog.Warn("knowledge merge: source not found, skipping", "slug", srcSlug)
+			continue
+		}
+		appended.WriteString("\n\n---\n\n## Merged: ")
+		appended.WriteString(srcTitle)
+		appended.WriteString("\n\n*Originally ")
+		appended.WriteString(srcSlug)
+		appended.WriteString(", last updated ")
+		appended.WriteString(srcUpdated)
+		appended.WriteString("*\n\n")
+		appended.WriteString(srcContent)
+		for _, t := range srcTags {
+			tagSet[strings.ToLower(strings.TrimSpace(t))] = true
+		}
+		merged = append(merged, srcSlug)
+	}
+
+	if len(merged) == 0 {
+		writeProblem(w, req, http.StatusBadRequest, "no valid source notes to merge", "")
+		return
+	}
+
+	extraTags := make([]string, 0, len(tagSet))
+	for t := range tagSet {
+		if t != "" {
+			extraTags = append(extraTags, t)
+		}
+	}
+	sort.Strings(extraTags)
+
+	// The array concat + DISTINCT keeps the target's own tags first and adds
+	// only what the sources contribute.
+	if _, err := tx.Exec(ctx, `
+		UPDATE knowledge_entities
+		SET content   = content || $2,
+		    tags      = ARRAY(SELECT DISTINCT unnest(COALESCE(tags,'{}') || $3::text[])),
+		    edited_by = $4,
+		    updated_at = now()
+		WHERE entity_id = $1`,
+		targetID, appended.String(), extraTags, actorLabel); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "merge write failed", err.Error())
+		return
+	}
+
+	for _, srcSlug := range merged {
+		if _, err := tx.Exec(ctx, `
+			UPDATE knowledge_entities ke
+			SET deleted_at = now(), edited_by = $2
+			FROM entities e
+			WHERE e.id = ke.entity_id AND (e.slug = $1 OR e.id::text = $1)`,
+			srcSlug, actorLabel); err != nil {
+			writeProblem(w, req, http.StatusInternalServerError, "source delete failed", err.Error())
+			return
+		}
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "commit failed", err.Error())
+		return
+	}
+
+	slog.Info("knowledge merged", "target", body.Target, "sources", merged, "actor", actorLabel)
+	writeJSON(w, map[string]any{"ok": true, "merged": merged, "tags_added": extraTags})
+}
+
+// lowerAll is the case-folding helper the tag queries compare against.
+func lowerAll(in []string) []string {
+	out := make([]string, len(in))
+	for i, s := range in {
+		out[i] = strings.ToLower(strings.TrimSpace(s))
+	}
+	return out
+}

internal/httpapi/knowledge_write.go

@@ -0,0 +1,659 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"errors"
+	"log/slog"
+	"net/http"
+	"net/url"
+	"regexp"
+	"strings"
+
+	"github.com/go-chi/chi/v5"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// Operator-facing write path for the knowledge base. Until this file, the
+// only way anything reached knowledge_entities was the MCP tool
+// upsert_knowledge (internal/mcp/server.go) — an agent-only surface. The web
+// UI could search and read but never create, correct, or remove a note, so
+// the operator's own knowledge had nowhere to go and an agent mistake had no
+// fix short of psql.
+//
+// All routes here are non-OpenAPI custom routes, consistent with the existing
+// knowledge read routes (see the carve-out block in server.go): they trade in
+// raw markdown and ad-hoc aggregates rather than generated schema types.
+//
+// Deletion is soft (deleted_at) — see migrations/022_knowledge_revisions.up.sql
+// for why — so every read path in this file filters on `ke.deleted_at IS NULL`.
+
+// knowledgeSlugSegmentRe strips a title down to a single slug segment.
+// Mirrors knowledgeSlugRe in internal/mcp/server.go; duplicated rather than
+// exported across the package boundary because the two callers namespace
+// their output differently (see knowledgeSlugFor).
+var knowledgeSlugSegmentRe = regexp.MustCompile(`[^a-z0-9]+`)
+
+// knowledgeSlugFor builds `<kind>:<folder>/<title-slug>`. The MCP tool's
+// equivalent hardcodes the `nomos/` folder; operator-created notes need to
+// land somewhere else so the navigator tree can tell at a glance who wrote
+// what, and so an operator note can never collide with an agent note that
+// happens to share a title.
+func knowledgeSlugFor(kind, folder, title string) string {
+	s := strings.ToLower(strings.TrimSpace(title))
+	s = knowledgeSlugSegmentRe.ReplaceAllString(s, "-")
+	s = strings.Trim(s, "-")
+	if s == "" {
+		s = "note"
+	}
+	if len(s) > 80 {
+		s = s[:80]
+	}
+	folder = strings.Trim(strings.ToLower(strings.TrimSpace(folder)), "/")
+	folder = knowledgeSlugSegmentRe.ReplaceAllString(folder, "-")
+	folder = strings.Trim(folder, "-")
+	if folder == "" {
+		folder = "operator"
+	}
+	return kind + ":" + folder + "/" + s
+}
+
+// validKnowledgeKind mirrors the three entity types that knowledge_entities
+// rows are allowed to hang off (see upsert_knowledge's own check).
+func validKnowledgeKind(kind string) bool {
+	switch kind {
+	case "document", "investigation", "runbook":
+		return true
+	}
+	return false
+}
+
+// resolveKnowledgeEntity maps an id-or-slug path segment to the entity id of
+// a live (non-deleted) knowledge note. Returns pgx.ErrNoRows when there's no
+// such note, which callers turn into a 404.
+func (s *Server) resolveKnowledgeEntity(ctx context.Context, idOrSlug string) (uuid.UUID, error) {
+	var id uuid.UUID
+	err := s.pool.QueryRow(ctx, `
+		SELECT ke.entity_id
+		FROM knowledge_entities ke
+		JOIN entities e ON e.id = ke.entity_id
+		WHERE (e.slug = $1 OR e.id::text = $1)
+		  AND ke.deleted_at IS NULL`, idOrSlug).Scan(&id)
+	return id, err
+}
+
+// resolveKnowledgeEntityAny is resolveKnowledgeEntity without the
+// deleted_at filter — for the one read path (revisions) that must still work
+// on a deleted note. The whole point of soft-delete is that a note's history
+// stays inspectable after removal (e.g. to confirm what was lost before
+// restoring it); requiring the note to be live first would defeat that.
+func (s *Server) resolveKnowledgeEntityAny(ctx context.Context, idOrSlug string) (uuid.UUID, error) {
+	var id uuid.UUID
+	err := s.pool.QueryRow(ctx, `
+		SELECT ke.entity_id
+		FROM knowledge_entities ke
+		JOIN entities e ON e.id = ke.entity_id
+		WHERE e.slug = $1 OR e.id::text = $1`, idOrSlug).Scan(&id)
+	return id, err
+}
+
+// pathParam pulls a chi URL param and percent-decodes it. Knowledge slugs
+// contain both ':' and '/' (e.g. "document:containers/101-jellyfin"), so they
+// reach the handler still encoded — chi.URLParam does no decoding of its own
+// on manually-registered routes (unlike the OpenAPI-generated ones, which
+// decode via runtime.BindStyledParameterWithOptions).
+func pathParam(req *http.Request, name string) (string, error) {
+	return url.PathUnescape(chi.URLParam(req, name))
+}
+
+// serveKnowledgeList returns every live note without its body — the backing
+// data for the wiki navigator tree. Distinct from /knowledge/recent, which
+// caps at 200 and exists to answer "what changed lately" for the stats view:
+// the tree needs the complete set, and needs the linked-entity slugs so it
+// can offer a group-by-entity arrangement without N+1 fetches.
+//
+// Body text is deliberately excluded — with ~100 notes averaging ~1 KB the
+// full payload would be ~100 KB per app open, to render a list that shows
+// only titles.
+func (s *Server) serveKnowledgeList(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	type item struct {
+		ID        string   `json:"id"`
+		Slug      string   `json:"slug"`
+		Title     string   `json:"title"`
+		Kind      string   `json:"kind"`
+		Source    string   `json:"source"`
+		EditedBy  string   `json:"edited_by"`
+		Tags      []string `json:"tags"`
+		About     []string `json:"about"`
+		Size      int      `json:"size"`
+		UpdatedAt string   `json:"updated_at"`
+		CreatedAt string   `json:"created_at"`
+		Revisions int      `json:"revisions"`
+	}
+
+	// The `about` aggregate mirrors GetEntityKnowledge's first UNION branch
+	// (documents/about edges) — the 'procedure-for' branch is left out here
+	// because it joins against entity *types* rather than entities and can't
+	// produce a per-note slug list.
+	rows, err := s.pool.Query(ctx, `
+		SELECT e.id::text, e.slug, ke.title, e.type, COALESCE(ke.source,''),
+		       COALESCE(ke.edited_by,''), COALESCE(ke.tags, '{}'),
+		       COALESCE((
+		         SELECT array_agg(DISTINCT t.slug)
+		         FROM relationships r
+		         JOIN entities t ON t.id = r.target_id
+		         WHERE r.source_id = ke.entity_id
+		           AND r.valid_to IS NULL
+		           AND r.type IN ('documents', 'about')
+		       ), '{}'),
+		       length(ke.content),
+		       ke.updated_at::text, ke.created_at::text,
+		       (SELECT count(*) FROM knowledge_revisions kr WHERE kr.entity_id = ke.entity_id)
+		FROM knowledge_entities ke
+		JOIN entities e ON e.id = ke.entity_id
+		WHERE ke.deleted_at IS NULL
+		ORDER BY ke.updated_at DESC`)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	items := []item{}
+	for rows.Next() {
+		var it item
+		if err := rows.Scan(&it.ID, &it.Slug, &it.Title, &it.Kind, &it.Source,
+			&it.EditedBy, &it.Tags, &it.About, &it.Size,
+			&it.UpdatedAt, &it.CreatedAt, &it.Revisions); err != nil {
+			slog.Error("httpapi: knowledge/list row scan failed", "error", err)
+			continue
+		}
+		items = append(items, it)
+	}
+
+	writeJSON(w, map[string]any{"items": items})
+}
+
+// serveKnowledgeTrash lists soft-deleted notes — the counterpart to
+// serveKnowledgeList, and what the "restore" affordance in the UI browses.
+// Without this, a deleted note is invisible from every list endpoint
+// (correctly — they all filter deleted_at) with no way to even discover it
+// exists to restore.
+func (s *Server) serveKnowledgeTrash(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT e.slug, ke.title, e.type, COALESCE(ke.edited_by,''), ke.deleted_at::text
+		FROM knowledge_entities ke
+		JOIN entities e ON e.id = ke.entity_id
+		WHERE ke.deleted_at IS NOT NULL
+		ORDER BY ke.deleted_at DESC`)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	type item struct {
+		Slug      string `json:"slug"`
+		Title     string `json:"title"`
+		Kind      string `json:"kind"`
+		DeletedBy string `json:"deleted_by"`
+		DeletedAt string `json:"deleted_at"`
+	}
+	items := []item{}
+	for rows.Next() {
+		var it item
+		if err := rows.Scan(&it.Slug, &it.Title, &it.Kind, &it.DeletedBy, &it.DeletedAt); err != nil {
+			slog.Error("httpapi: knowledge/trash row scan failed", "error", err)
+			continue
+		}
+		items = append(items, it)
+	}
+
+	writeJSON(w, map[string]any{"items": items})
+}
+
+// knowledgeWriteBody is the shared request shape for create and update.
+// Every field is a pointer so update can distinguish "not supplied" (leave
+// alone) from "supplied empty" (clear it) — a PUT that only changes tags
+// must not blank the body.
+type knowledgeWriteBody struct {
+	Title   *string   `json:"title"`
+	Content *string   `json:"content"`
+	Kind    *string   `json:"kind"`
+	Tags    *[]string `json:"tags"`
+	Folder  *string   `json:"folder"`
+	About   *[]string `json:"about"`
+}
+
+// serveCreateKnowledge creates a note plus its backing entity, and links it
+// to whatever entities it's about.
+func (s *Server) serveCreateKnowledge(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	var body knowledgeWriteBody
+	if err := json.NewDecoder(req.Body).Decode(&body); err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid request body", err.Error())
+		return
+	}
+
+	title := strings.TrimSpace(deref(body.Title))
+	content := strings.TrimSpace(deref(body.Content))
+	if title == "" || content == "" {
+		writeProblem(w, req, http.StatusBadRequest, "title and content are required", "")
+		return
+	}
+	kind := deref(body.Kind)
+	if kind == "" {
+		kind = "document"
+	}
+	if !validKnowledgeKind(kind) {
+		writeProblem(w, req, http.StatusBadRequest, "invalid kind",
+			"kind must be document, investigation, or runbook")
+		return
+	}
+	tags := normalizeTags(derefSlice(body.Tags))
+	slug := knowledgeSlugFor(kind, deref(body.Folder), title)
+	_, actorLabel := actorInfo(ctx)
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "begin failed", err.Error())
+		return
+	}
+	defer tx.Rollback(ctx)
+
+	docID, _ := uuid.NewV7()
+	// ON CONFLICT covers the soft-deleted case: the entity row survives a
+	// delete, so recreating a note under the same slug must reuse it rather
+	// than fail the unique constraint.
+	if err := tx.QueryRow(ctx, `
+		INSERT INTO entities (id, slug, type, name, attributes)
+		VALUES ($1, $2, $3, $4, '{}')
+		ON CONFLICT (slug) DO UPDATE SET name = EXCLUDED.name, updated_at = now()
+		RETURNING id`, docID, slug, kind, title).Scan(&docID); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "create entity failed", err.Error())
+		return
+	}
+
+	// Refuse to silently overwrite an existing LIVE note — upsert_knowledge
+	// (the MCP tool) deliberately upserts by title (the agent re-records the
+	// same finding as it learns more), but an operator hitting "create" with
+	// a colliding title almost certainly means to write something new.
+	//
+	// The `WHERE knowledge_entities.deleted_at IS NOT NULL` guard makes this
+	// check atomic with the write, rather than a separate SELECT before it:
+	// a plain pre-check has a TOCTOU race where two concurrent creates of
+	// the same title can both pass the check and then both proceed to
+	// INSERT ON CONFLICT DO UPDATE, silently clobbering each other. Here,
+	// the UPDATE branch only actually applies when the conflicting row is
+	// soft-deleted (a legitimate "resurrect" case). When it isn't, the row
+	// is left untouched, RETURNING yields no row, and pgx.ErrNoRows below
+	// becomes the 409 — the collision can never be missed, no matter how
+	// the two writers interleave.
+	var wroteID uuid.UUID
+	err = tx.QueryRow(ctx, `
+		INSERT INTO knowledge_entities
+			(entity_id, title, content, source, tags, edited_by, updated_at, deleted_at)
+		VALUES ($1, $2, $3, $4, $5, $4, now(), NULL)
+		ON CONFLICT (entity_id) DO UPDATE
+		  SET title = EXCLUDED.title, content = EXCLUDED.content,
+		      tags = EXCLUDED.tags, edited_by = EXCLUDED.edited_by,
+		      updated_at = now(), deleted_at = NULL
+		  WHERE knowledge_entities.deleted_at IS NOT NULL
+		RETURNING entity_id`,
+		docID, title, content, actorLabel, tags).Scan(&wroteID)
+	if errors.Is(err, pgx.ErrNoRows) {
+		writeProblem(w, req, http.StatusConflict, "a note with this title already exists", slug)
+		return
+	} else if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "write knowledge failed", err.Error())
+		return
+	}
+
+	linked := s.linkKnowledgeAbout(ctx, tx, docID, derefSlice(body.About))
+
+	if err := tx.Commit(ctx); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "commit failed", err.Error())
+		return
+	}
+
+	slog.Info("knowledge created", "slug", slug, "kind", kind, "actor", actorLabel, "linked", linked)
+	// Content-Type before WriteHeader — setting it after is a no-op, the
+	// status line is already on the wire.
+	w.Header().Set("Content-Type", "application/json")
+	w.WriteHeader(http.StatusCreated)
+	if err := json.NewEncoder(w).Encode(map[string]any{
+		"slug": slug, "id": docID.String(), "linked": linked,
+	}); err != nil {
+		slog.Error("httpapi: json encode failed", "error", err)
+	}
+}
+
+// serveUpdateKnowledge edits a live note in place. The prior version is
+// captured by the trg_knowledge_revision trigger, not by this handler — see
+// the migration for why that lives in the database.
+//
+// Note the slug is intentionally NOT recomputed when the title changes:
+// slugs are the wiki's stable link target ([[slug]] references, relationship
+// rows, bookmarked window ids), and silently re-slugging on a typo fix would
+// break every inbound link.
+func (s *Server) serveUpdateKnowledge(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	idOrSlug, err := pathParam(req, "id")
+	if err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid id", err.Error())
+		return
+	}
+
+	var body knowledgeWriteBody
+	if err := json.NewDecoder(req.Body).Decode(&body); err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid request body", err.Error())
+		return
+	}
+	if body.Title == nil && body.Content == nil && body.Tags == nil && body.About == nil {
+		writeProblem(w, req, http.StatusBadRequest, "nothing to update",
+			"supply at least one of title, content, tags, about")
+		return
+	}
+	if body.Title != nil && strings.TrimSpace(*body.Title) == "" {
+		writeProblem(w, req, http.StatusBadRequest, "title cannot be empty", "")
+		return
+	}
+	if body.Content != nil && strings.TrimSpace(*body.Content) == "" {
+		writeProblem(w, req, http.StatusBadRequest, "content cannot be empty", "")
+		return
+	}
+
+	entityID, err := s.resolveKnowledgeEntity(ctx, idOrSlug)
+	if err != nil {
+		writeProblem(w, req, http.StatusNotFound, "no such knowledge note", "")
+		return
+	}
+	_, actorLabel := actorInfo(ctx)
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "begin failed", err.Error())
+		return
+	}
+	defer tx.Rollback(ctx)
+
+	// COALESCE keeps unsupplied fields untouched; edited_by and updated_at
+	// always move so the UI can show who last touched it. The trigger only
+	// snapshots when title/content/tags actually differ, so a no-op save
+	// doesn't manufacture a revision.
+	var newTitle *string
+	if body.Title != nil {
+		t := strings.TrimSpace(*body.Title)
+		newTitle = &t
+	}
+	var newContent *string
+	if body.Content != nil {
+		c := strings.TrimSpace(*body.Content)
+		newContent = &c
+	}
+	var newTags *[]string
+	if body.Tags != nil {
+		t := normalizeTags(*body.Tags)
+		newTags = &t
+	}
+
+	if _, err := tx.Exec(ctx, `
+		UPDATE knowledge_entities
+		SET title      = COALESCE($2, title),
+		    content    = COALESCE($3, content),
+		    tags       = COALESCE($4, tags),
+		    edited_by  = $5,
+		    updated_at = now()
+		WHERE entity_id = $1`,
+		entityID, newTitle, newContent, newTags, actorLabel); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "update failed", err.Error())
+		return
+	}
+
+	// Keep the entity's display name in step with the note title — the graph
+	// and the fleet table read entities.name, and leaving it stale is exactly
+	// the drift this app exists to fight.
+	if newTitle != nil {
+		if _, err := tx.Exec(ctx,
+			`UPDATE entities SET name = $2, updated_at = now() WHERE id = $1`,
+			entityID, *newTitle); err != nil {
+			writeProblem(w, req, http.StatusInternalServerError, "rename entity failed", err.Error())
+			return
+		}
+	}
+
+	// About is replace-semantics, not merge: the editor presents the full
+	// link set, so an absent slug means the operator removed it. Existing
+	// edges are closed (valid_to) rather than deleted, preserving history.
+	var linked []string
+	if body.About != nil {
+		if _, err := tx.Exec(ctx, `
+			UPDATE relationships SET valid_to = now()
+			WHERE source_id = $1 AND valid_to IS NULL AND type IN ('documents', 'about')`,
+			entityID); err != nil {
+			writeProblem(w, req, http.StatusInternalServerError, "unlink failed", err.Error())
+			return
+		}
+		linked = s.linkKnowledgeAbout(ctx, tx, entityID, *body.About)
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "commit failed", err.Error())
+		return
+	}
+
+	slog.Info("knowledge updated", "entity_id", entityID, "actor", actorLabel)
+	// `linked` lets the caller diff against what it submitted and warn about
+	// any slug that didn't resolve — see linkKnowledgeAbout: a typo'd entity
+	// slug otherwise fails with nothing but a server-side slog.Warn, so the
+	// operator gets no feedback that one of their About links didn't take.
+	writeJSON(w, map[string]any{"ok": true, "linked": linked})
+}
+
+// serveDeleteKnowledge soft-deletes a note. The row, its revision trail and
+// its entity all survive; only the deleted_at stamp changes, and every read
+// path filters on it.
+func (s *Server) serveDeleteKnowledge(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	idOrSlug, err := pathParam(req, "id")
+	if err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid id", err.Error())
+		return
+	}
+	entityID, err := s.resolveKnowledgeEntity(ctx, idOrSlug)
+	if err != nil {
+		writeProblem(w, req, http.StatusNotFound, "no such knowledge note", "")
+		return
+	}
+	_, actorLabel := actorInfo(ctx)
+
+	// Snapshot the live version before tombstoning. The trigger fires on
+	// title/content/tags changes only, and a delete changes none of them —
+	// without this the most recent version would be the one version missing
+	// from the history if the note is later restored.
+	if _, err := s.pool.Exec(ctx, `
+		INSERT INTO knowledge_revisions
+			(entity_id, title, content, source, tags, edited_by, version_at)
+		SELECT entity_id, title, content, source, tags, COALESCE(edited_by,''), updated_at
+		FROM knowledge_entities WHERE entity_id = $1`, entityID); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "snapshot failed", err.Error())
+		return
+	}
+	if _, err := s.pool.Exec(ctx, `
+		UPDATE knowledge_entities SET deleted_at = now(), edited_by = $2
+		WHERE entity_id = $1`, entityID, actorLabel); err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "delete failed", err.Error())
+		return
+	}
+
+	slog.Info("knowledge deleted", "entity_id", entityID, "actor", actorLabel)
+	writeJSON(w, map[string]any{"ok": true})
+}
+
+// serveRestoreKnowledge undoes a soft delete. The counterpart to
+// serveDeleteKnowledge — without it, "recoverable by clearing the column"
+// (see the migration) would only be true via psql, which isn't a real
+// recovery path for an operator using the wiki.
+func (s *Server) serveRestoreKnowledge(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	idOrSlug, err := pathParam(req, "id")
+	if err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid id", err.Error())
+		return
+	}
+	entityID, err := s.resolveKnowledgeEntityAny(ctx, idOrSlug)
+	if err != nil {
+		writeProblem(w, req, http.StatusNotFound, "no such knowledge note", "")
+		return
+	}
+	_, actorLabel := actorInfo(ctx)
+
+	ct, err := s.pool.Exec(ctx, `
+		UPDATE knowledge_entities SET deleted_at = NULL, edited_by = $2
+		WHERE entity_id = $1 AND deleted_at IS NOT NULL`, entityID, actorLabel)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "restore failed", err.Error())
+		return
+	}
+	if ct.RowsAffected() == 0 {
+		writeProblem(w, req, http.StatusConflict, "note is not deleted", "")
+		return
+	}
+
+	slog.Info("knowledge restored", "entity_id", entityID, "actor", actorLabel)
+	writeJSON(w, map[string]any{"ok": true})
+}
+
+// serveKnowledgeRevisions returns the note's superseded versions, newest
+// first. Bodies are included: revisions are small (~1 KB) and few, and the
+// diff view needs both sides anyway — paginating would cost a round trip per
+// comparison to save nothing.
+func (s *Server) serveKnowledgeRevisions(w http.ResponseWriter, req *http.Request) {
+	ctx := req.Context()
+
+	idOrSlug, err := pathParam(req, "id")
+	if err != nil {
+		writeProblem(w, req, http.StatusBadRequest, "invalid id", err.Error())
+		return
+	}
+	entityID, err := s.resolveKnowledgeEntityAny(ctx, idOrSlug)
+	if err != nil {
+		writeProblem(w, req, http.StatusNotFound, "no such knowledge note", "")
+		return
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT id, title, content, COALESCE(edited_by,''), COALESCE(tags,'{}'),
+		       version_at::text, revised_at::text
+		FROM knowledge_revisions
+		WHERE entity_id = $1
+		ORDER BY version_at DESC`, entityID)
+	if err != nil {
+		writeProblem(w, req, http.StatusInternalServerError, "query failed", err.Error())
+		return
+	}
+	defer rows.Close()
+
+	type revision struct {
+		ID        int64    `json:"id"`
+		Title     string   `json:"title"`
+		Content   string   `json:"content"`
+		EditedBy  string   `json:"edited_by"`
+		Tags      []string `json:"tags"`
+		VersionAt string   `json:"version_at"`
+		RevisedAt string   `json:"revised_at"`
+	}
+	items := []revision{}
+	for rows.Next() {
+		var r revision
+		if err := rows.Scan(&r.ID, &r.Title, &r.Content, &r.EditedBy, &r.Tags,
+			&r.VersionAt, &r.RevisedAt); err != nil {
+			slog.Error("httpapi: knowledge/revisions row scan failed", "error", err)
+			continue
+		}
+		items = append(items, r)
+	}
+
+	writeJSON(w, map[string]any{"items": items})
+}
+
+// linkKnowledgeAbout points a note at the entities it concerns, skipping
+// slugs that don't resolve and edges that already exist. Returns the slugs
+// actually linked so the caller can report what stuck — a typo'd slug is a
+// silent no-op otherwise.
+func (s *Server) linkKnowledgeAbout(ctx context.Context, tx pgx.Tx, docID uuid.UUID, slugs []string) []string {
+	linked := []string{}
+	for _, raw := range slugs {
+		slug := strings.TrimSpace(raw)
+		if slug == "" {
+			continue
+		}
+		var targetID uuid.UUID
+		if err := tx.QueryRow(ctx, `SELECT id FROM entities WHERE slug = $1`, slug).Scan(&targetID); err != nil {
+			slog.Warn("knowledge: about slug not found, skipping", "slug", slug)
+			continue
+		}
+		if _, err := tx.Exec(ctx, `
+			INSERT INTO relationships (source_id, target_id, type, attributes, valid_from)
+			SELECT $1, $2, 'about', '{"by":"operator"}'::jsonb, now()
+			WHERE NOT EXISTS (
+				SELECT 1 FROM relationships
+				WHERE source_id = $1 AND target_id = $2 AND type = 'about' AND valid_to IS NULL)`,
+			docID, targetID); err != nil {
+			slog.Warn("knowledge: link failed", "slug", slug, "error", err)
+			continue
+		}
+		linked = append(linked, slug)
+	}
+	return linked
+}
+
+// normalizeTags trims, lowercases and de-duplicates while preserving order.
+// Lowercasing is the fix for the casing drift already in the data — `oom`
+// and `OOM` were separate tags on separate notes, so neither tag page showed
+// the full set. Applied on every write so the split can't reopen.
+func normalizeTags(in []string) []string {
+	seen := map[string]bool{}
+	out := []string{}
+	for _, t := range in {
+		t = strings.ToLower(strings.TrimSpace(t))
+		if t == "" || seen[t] {
+			continue
+		}
+		seen[t] = true
+		out = append(out, t)
+	}
+	return out
+}
+
+func deref(p *string) string {
+	if p == nil {
+		return ""
+	}
+	return *p
+}
+
+func derefSlice(p *[]string) []string {
+	if p == nil {
+		return nil
+	}
+	return *p
+}
+
+// writeJSON is the success-path counterpart to writeProblem, so the handlers
+// in this file don't each repeat the header/encode dance.
+func writeJSON(w http.ResponseWriter, v any) {
+	w.Header().Set("Content-Type", "application/json")
+	if err := json.NewEncoder(w).Encode(v); err != nil {
+		slog.Error("httpapi: json encode failed", "error", err)
+	}
+}

internal/httpapi/metrics.go

@@ -0,0 +1,180 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+	"time"
+
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/jackc/pgx/v5/pgtype"
+)
+
+// ─── Metrics ───────────────────────────────────────────────────────────
+
+func (s *Server) QueryMetrics(ctx context.Context, req gen.QueryMetricsRequestObject) (gen.QueryMetricsResponseObject, error) {
+	if req.Params.EntityId == nil || *req.Params.EntityId == "" {
+		return nil, fmt.Errorf("%w: entity_id is required", domain.ErrInvalidInput)
+	}
+	entityID, err := s.resolveEntityID(ctx, *req.Params.EntityId)
+	if err != nil {
+		return nil, err
+	}
+
+	from := time.Now().Add(-24 * time.Hour)
+	if req.Params.From != nil {
+		from = *req.Params.From
+	}
+	to := time.Now()
+	if req.Params.To != nil {
+		to = *req.Params.To
+	}
+
+	var metricNames []string
+	if req.Params.Metric != nil && len(*req.Params.Metric) > 0 {
+		metricNames = *req.Params.Metric
+	} else {
+		// metric omitted: report every metric recorded for this entity in range.
+		rows, err := s.pool.Query(ctx, `
+			SELECT DISTINCT metric FROM metric_samples
+			WHERE entity_id = $1 AND ts >= $2 AND ts <= $3
+			ORDER BY metric`, entityID, from, to)
+		if err != nil {
+			return nil, err
+		}
+		for rows.Next() {
+			var name string
+			if err := rows.Scan(&name); err != nil {
+				rows.Close()
+				return nil, err
+			}
+			metricNames = append(metricNames, name)
+		}
+		if err := rows.Err(); err != nil {
+			return nil, err
+		}
+	}
+
+	items := []gen.MetricSeries{}
+	for _, metricName := range metricNames {
+		series := gen.MetricSeries{
+			EntityId: entityID.String(),
+			Metric:   metricName,
+			Rollup:   gen.MetricSeriesRollupRaw,
+		}
+
+		rows, err := s.pool.Query(ctx, `
+			SELECT ts, value
+			FROM metric_samples
+			WHERE entity_id = $1 AND metric = $2
+			  AND ts >= $3 AND ts <= $4
+			ORDER BY ts ASC`,
+			entityID, metricName, from, to)
+		if err != nil {
+			return nil, err
+		}
+
+		samples := []struct {
+			Avg   *float32  `json:"avg"`
+			Count *int      `json:"count"`
+			Max   *float32  `json:"max"`
+			Min   *float32  `json:"min"`
+			Ts    time.Time `json:"ts"`
+			Value *float32  `json:"value"`
+		}{}
+
+		for rows.Next() {
+			var ts time.Time
+			var val float64
+			if err := rows.Scan(&ts, &val); err != nil {
+				rows.Close()
+				return nil, err
+			}
+			f := float32(val)
+			samples = append(samples, struct {
+				Avg   *float32  `json:"avg"`
+				Count *int      `json:"count"`
+				Max   *float32  `json:"max"`
+				Min   *float32  `json:"min"`
+				Ts    time.Time `json:"ts"`
+				Value *float32  `json:"value"`
+			}{Value: &f, Ts: ts})
+		}
+		rows.Close()
+		if rows.Err() != nil {
+			return nil, rows.Err()
+		}
+
+		series.Samples = samples
+		items = append(items, series)
+	}
+
+	if items == nil {
+		items = []gen.MetricSeries{}
+	}
+	return gen.QueryMetrics200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) GetTrends(ctx context.Context, req gen.GetTrendsRequestObject) (gen.GetTrendsResponseObject, error) {
+	entityID, err := s.resolveEntityID(ctx, req.EntityId)
+	if err != nil {
+		return nil, err
+	}
+
+	from := time.Now().Add(-7 * 24 * time.Hour)
+	if req.Params.From != nil {
+		from = *req.Params.From
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT metric,
+		       ROUND(avg(value)::numeric, 2) AS avg_val,
+		       ROUND(stddev(value)::numeric, 2) AS std_val,
+		       count(*) AS sample_count,
+		       ROUND(regr_slope(value, EXTRACT(EPOCH FROM ts)::numeric)::numeric, 4) AS slope
+		FROM metric_samples
+		WHERE entity_id = $1 AND ts >= $2
+		GROUP BY metric
+		ORDER BY metric`, entityID, from)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Trend{}
+	for rows.Next() {
+		var t gen.Trend
+		var avgVal, stdVal, slopeNum pgtype.Numeric
+		var sampleCount int
+		if err := rows.Scan(&t.Metric, &avgVal, &stdVal, &sampleCount, &slopeNum); err != nil {
+			return nil, err
+		}
+
+		// Determine direction.
+		if slopeNum.Valid {
+			f, _ := slopeNum.Float64Value()
+			t.Slope = float32Ptr(float32(f.Float64))
+			if f.Float64 > 0.01 {
+				t.Direction = gen.TrendDirectionImproving
+			} else if f.Float64 < -0.01 {
+				t.Direction = gen.TrendDirectionDegrading
+			} else {
+				t.Direction = gen.TrendDirectionStable
+			}
+		} else {
+			t.Direction = gen.TrendDirectionUnknown
+		}
+		items = append(items, t)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.Trend{}
+	}
+	return gen.GetTrends200JSONResponse{Items: items}, nil
+}
+
+func float32Ptr(f float32) *float32 {
+	return &f
+}

internal/httpapi/patterns.go

@@ -0,0 +1,124 @@
+package httpapi
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/jackc/pgx/v5"
+)
+
+// ─── Patterns ──────────────────────────────────────────────────────────
+
+func (s *Server) ListPatterns(ctx context.Context, req gen.ListPatternsRequestObject) (gen.ListPatternsResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+	rows, err := s.pool.Query(ctx, `
+		SELECT p.entity_id, e.slug, p.applies_type, p.action, p.pattern, p.confidence,
+		       p.evidence_count, p.success_count, p.failure_count, p.status,
+		       p.quarantined, p.version, p.last_validated_at
+		FROM patterns p
+		JOIN entities e ON e.id = p.entity_id
+		WHERE ($1::text IS NULL OR p.status = $1)
+		  AND ($2::text IS NULL OR p.applies_type = $2)
+		  AND ($3::text IS NULL OR p.action = $3)
+		ORDER BY p.applies_type, p.action
+		LIMIT $4`,
+		req.Params.Status, req.Params.EntityType, req.Params.Action, limit+1)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Pattern{}
+	for rows.Next() {
+		var p gen.Pattern
+		if err := rows.Scan(&p.Id, &p.Slug, &p.AppliesType, &p.Action, &p.Pattern,
+			&p.Confidence, &p.EvidenceCount, &p.SuccessCount, &p.FailureCount,
+			&p.Status, &p.Quarantined, &p.Version, &p.LastValidatedAt); err != nil {
+			return nil, err
+		}
+		items = append(items, p)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	if items == nil {
+		items = []gen.Pattern{}
+	}
+	return gen.ListPatterns200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) PatchPattern(ctx context.Context, req gen.PatchPatternRequestObject) (gen.PatchPatternResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+	q := sqlcgen.New(tx)
+
+	if req.Body.Status != nil {
+		status := string(*req.Body.Status)
+		if err := q.UpdatePatternStatus(ctx, sqlcgen.UpdatePatternStatusParams{
+			EntityID: id,
+			Status:   status,
+		}); err != nil {
+			if err == pgx.ErrNoRows {
+				return nil, fmt.Errorf("%w: pattern %s", domain.ErrNotFound, req.Id)
+			}
+			return nil, err
+		}
+	}
+
+	if req.Body.Quarantined != nil {
+		if err := q.UpdatePatternQuarantine(ctx, sqlcgen.UpdatePatternQuarantineParams{
+			EntityID:    id,
+			Quarantined: *req.Body.Quarantined,
+		}); err != nil {
+			return nil, err
+		}
+	}
+
+	// Re-read.
+	var p gen.Pattern
+	err = tx.QueryRow(ctx, `
+		SELECT entity_id, applies_type, action, pattern, confidence,
+		       evidence_count, success_count, failure_count, status,
+		       quarantined, version, last_validated_at
+		FROM patterns WHERE entity_id = $1`, id).
+		Scan(&p.Id, &p.AppliesType, &p.Action, &p.Pattern,
+			&p.Confidence, &p.EvidenceCount, &p.SuccessCount, &p.FailureCount,
+			&p.Status, &p.Quarantined, &p.Version, &p.LastValidatedAt)
+	if err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: pattern %s", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "patch",
+		&id, "PATCH", "/api/v1/patterns/"+req.Id, "",
+		nil,
+		map[string]any{"status": req.Body.Status, "quarantined": req.Body.Quarantined}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchPattern200JSONResponse(p), nil
+}

internal/httpapi/relationships.go

@@ -0,0 +1,122 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"strings"
+	"time"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+)
+
+// ─── Relationships ─────────────────────────────────────────────────────
+
+func (s *Server) CreateRelationship(ctx context.Context, req gen.CreateRelationshipRequestObject) (gen.CreateRelationshipResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	sourceID, err := s.resolveEntityID(ctx, req.Body.Source)
+	if err != nil {
+		return nil, err
+	}
+	targetID, err := s.resolveEntityID(ctx, req.Body.Target)
+	if err != nil {
+		return nil, err
+	}
+
+	attrsJSON := []byte("{}")
+	if req.Body.Attributes != nil {
+		attrsJSON, _ = json.Marshal(req.Body.Attributes)
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	_, err = tx.Exec(ctx, `
+		INSERT INTO relationships (source_id, target_id, type, attributes, valid_from)
+		VALUES ($1, $2, $3, $4, now())`,
+		sourceID, targetID, req.Body.Type, attrsJSON)
+	if err != nil {
+		if strings.Contains(err.Error(), "unique") || strings.Contains(err.Error(), "duplicate") {
+			return nil, fmt.Errorf("%w: relationship %s:%s:%s already exists",
+				domain.ErrAlreadyExists, req.Body.Source, req.Body.Type, req.Body.Target)
+		}
+		return nil, err
+	}
+
+	rel := gen.Relationship{
+		Source:    req.Body.Source,
+		Target:    req.Body.Target,
+		Type:      req.Body.Type,
+		ValidFrom: time.Now(),
+	}
+	if req.Body.Attributes != nil {
+		rel.Attributes = req.Body.Attributes
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "create",
+		nil, "POST", "/api/v1/relationships", "",
+		nil,
+		map[string]any{"source": req.Body.Source, "target": req.Body.Target, "type": req.Body.Type}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.CreateRelationship201JSONResponse(rel), nil
+}
+
+func (s *Server) EndRelationship(ctx context.Context, req gen.EndRelationshipRequestObject) (gen.EndRelationshipResponseObject, error) {
+	sourceID, err := s.resolveEntityID(ctx, req.Params.Source)
+	if err != nil {
+		return nil, err
+	}
+	targetID, err := s.resolveEntityID(ctx, req.Params.Target)
+	if err != nil {
+		return nil, err
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+
+	result, err := sqlcgen.New(tx).EndCurrentRelationship(ctx, sqlcgen.EndCurrentRelationshipParams{
+		SourceID: sourceID,
+		TargetID: targetID,
+		Type:     req.Params.RelType,
+	})
+	if err != nil {
+		return nil, err
+	}
+	if result == 0 {
+		return nil, fmt.Errorf("%w: active relationship %s:%s:%s",
+			domain.ErrNotFound, req.Params.Source, req.Params.RelType, req.Params.Target)
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, sqlcgen.New(tx), actorType, actor, "delete",
+		nil, "DELETE", "/api/v1/relationships", "",
+		nil,
+		map[string]any{"source": req.Params.Source, "target": req.Params.Target, "type": req.Params.RelType}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.EndRelationship204Response{}, nil
+}

internal/httpapi/risk_classes.go

@@ -0,0 +1,33 @@
+package httpapi
+
+import (
+	"context"
+
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+)
+
+// ─── Risk Classes ──────────────────────────────────────────────────────
+
+func (s *Server) ListRiskClasses(ctx context.Context, req gen.ListRiskClassesRequestObject) (gen.ListRiskClassesResponseObject, error) {
+	rows, err := s.pool.Query(ctx, `SELECT name, description, approval_required, autonomy_allowed FROM risk_classes ORDER BY name`)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.RiskClass{}
+	for rows.Next() {
+		var rc gen.RiskClass
+		if err := rows.Scan(&rc.Name, &rc.Description, &rc.ApprovalRequired, &rc.AutonomyAllowed); err != nil {
+			return nil, err
+		}
+		items = append(items, rc)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.RiskClass{}
+	}
+	return gen.ListRiskClasses200JSONResponse{Items: items}, nil
+}

internal/httpapi/server.go

@@ -97,6 +97,36 @@ func NewHandler(ctx context.Context, pool *db.Pool, cfg config.Config) http.Hand
 		MaxAge:         86400,
 	}))
 
+	// ─── Non-OpenAPI routes (carve-out) ────────────────────────────────
+	//
+	// These routes are registered manually on the chi router rather than
+	// generated from api/openapi.yaml. Each has a structural reason it
+	// can't go through the strict-server codegen:
+	//
+	//   /healthz               — infra liveness probe, no auth, no /api/v1 prefix
+	//   /api/v1/auth/oidc-*    — auth flow, must run before auth middleware
+	//   /oidc-callback         — standalone HTML page, not a JSON API
+	//   /api/v1/events/stream  — in OpenAPI but re-registered for SSE Flush()
+	//   /api/v1/knowledge/recent       — ad-hoc aggregation, no schema type yet
+	//   /api/v1/knowledge/content/{id} — returns raw markdown, not a gen type
+	//   /api/v1/knowledge/list         — full tree listing, ad-hoc aggregate
+	//   /api/v1/knowledge (POST)       — markdown in, no gen type
+	//   /api/v1/knowledge/content/{id} (PUT/DELETE) — markdown in, soft delete
+	//   /api/v1/knowledge/trash       — soft-deleted notes, ad-hoc
+	//   /api/v1/knowledge/restore/{id} — undo a soft delete, no gen type
+	//   /api/v1/knowledge/revisions/{id} — version history, no schema type
+	//   /api/v1/knowledge/tags{,/rename} — tag index + bulk rewrite
+	//   /api/v1/knowledge/duplicates   — trigram clustering, ad-hoc
+	//   /api/v1/knowledge/orphans      — derived maintenance view
+	//   /api/v1/knowledge/merge        — bulk fold-in, ad-hoc
+	//   /api/v1/activity/recent        — recency-ordered, not paginated
+	//   /api/v1/activity/session/{id}  — session-scoped aggregation
+	//   /api/v1/executions/{id}/logs   — streamed command output, no schema type
+	//   /api/v1/learning/timeline      — derived view, no backing schema type
+	//   /api/v1/learning/trend         — derived view, no backing schema type
+	//
+	// See .agents/dev/CONTRIBUTING.md §OpenAPI codegen for the policy.
+
 	// Liveness — no auth, no audit (plan SG18). Not exposed via Caddy.
 	r.Get("/healthz", func(w http.ResponseWriter, req *http.Request) {
 		ctx, cancel := context.WithTimeout(req.Context(), 2*time.Second)
@@ -173,23 +203,61 @@ func NewHandler(ctx context.Context, pool *db.Pool, cfg config.Config) http.Hand
 	// Custom (non-OpenAPI) route: recency-ordered knowledge + stats for the
 	// Knowledge page's "what the system has learned" view. Registered after
 	// HandlerWithOptions so it wins over any generated catch-all.
+	// (See "Non-OpenAPI routes" carve-out block above.)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/recent", s.serveRecentKnowledge)
 
 	// Custom (non-OpenAPI) route: full markdown content for a knowledge
 	// entity (document/investigation/runbook) by its own id or slug — the
 	// generated /api/v1/knowledge/{id} route (GetEntityKnowledge) answers a
 	// different question (knowledge referencing this entity), not this one.
+	// (See "Non-OpenAPI routes" carve-out block above.)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/content/{id}", s.serveKnowledgeContent)
 
+	// Custom (non-OpenAPI) routes: the operator-facing knowledge CRUD surface
+	// (see internal/httpapi/knowledge_write.go) and the drift tooling (see
+	// knowledge_drift.go). Before these, knowledge could only be written by
+	// the agent through the MCP upsert_knowledge tool — the web UI had no way
+	// to create, correct or retire a note.
+	//
+	// Registered on the base router rather than through the OpenAPI codegen
+	// for the same reason as the read routes above: they trade in raw
+	// markdown and ad-hoc aggregates, not generated schema types.
+	// (See "Non-OpenAPI routes" carve-out block above.)
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/list", s.serveKnowledgeList)
+	r.With(combinedAuth(cfg, false)).Post("/api/v1/knowledge", s.serveCreateKnowledge)
+	r.With(combinedAuth(cfg, false)).Put("/api/v1/knowledge/content/{id}", s.serveUpdateKnowledge)
+	r.With(combinedAuth(cfg, false)).Delete("/api/v1/knowledge/content/{id}", s.serveDeleteKnowledge)
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/trash", s.serveKnowledgeTrash)
+	r.With(combinedAuth(cfg, false)).Post("/api/v1/knowledge/restore/{id}", s.serveRestoreKnowledge)
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/revisions/{id}", s.serveKnowledgeRevisions)
+
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/tags", s.serveKnowledgeTags)
+	r.With(combinedAuth(cfg, false)).Post("/api/v1/knowledge/tags/rename", s.serveRenameKnowledgeTag)
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/duplicates", s.serveKnowledgeDuplicates)
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/knowledge/orphans", s.serveKnowledgeOrphans)
+	r.With(combinedAuth(cfg, false)).Post("/api/v1/knowledge/merge", s.serveMergeKnowledge)
+
+	// Drift audit: read-only DB-side report of orphan checks, checks on
+	// retired targets, stuck down/unknown probes, unmonitored declared types,
+	// and dangling edges. Companion to the knowledge-graph-audit skill.
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/audit/drift", s.serveAuditDrift)
+
 	// Custom (non-OpenAPI) routes: the global activity feed (recency-ordered,
 	// unlike ListExecutions which sorts by target for pagination) and the
 	// per-session "what did this session do" digest.
+	// (See "Non-OpenAPI routes" carve-out block above.)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/activity/recent", s.serveRecentActivity)
+	// Streamed command output for one execution — a projection over
+	// execution_logs with no schema type yet (same carve-out rationale as
+	// /activity/recent above). Nests cleanly under the generated
+	// /executions/{id} subtree: chi accepts sibling children on a param node.
+	r.With(combinedAuth(cfg, false)).Get("/api/v1/executions/{id}/logs", s.serveExecutionLogs)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/activity/session/{id}", s.serveSessionDigest)
 
 	// Learning view: capability timeline + success trend, both derived from
 	// executions (real, growing data) rather than the patterns/skills tables,
 	// which are correctly modeled but have no writers anywhere yet.
+	// (See "Non-OpenAPI routes" carve-out block above.)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/learning/timeline", s.serveLearningTimeline)
 	r.With(combinedAuth(cfg, false)).Get("/api/v1/learning/trend", s.serveLearningTrend)
 
@@ -326,10 +394,10 @@ func staticTokenActor(cfg config.Config, raw string) (actor, bool) {
 // jwtVerificationKey holds a parsed RSA public key or HMAC secret for JWT
 // verification, identified by its key ID (kid).
 type jwtVerificationKey struct {
-	Kid     string
-	Alg     string
-	Key     any // *rsa.PublicKey or []byte for HMAC
-	IsHMAC  bool
+	Kid    string
+	Alg    string
+	Key    any // *rsa.PublicKey or []byte for HMAC
+	IsHMAC bool
 }
 
 // discoverJWKSURI fetches the OIDC discovery document and extracts the
@@ -575,8 +643,8 @@ func resolveOIDCTokenURL(issuer string) string {
 func (s *Server) serveOIDCConfig(w http.ResponseWriter, _ *http.Request, cfg config.Config) {
 	w.Header().Set("Content-Type", "application/json")
 	json.NewEncoder(w).Encode(map[string]string{
-		"issuer":                cfg.OIDCIssuer,
-		"client_id":             cfg.OIDCClientID,
+		"issuer":                 cfg.OIDCIssuer,
+		"client_id":              cfg.OIDCClientID,
 		"authorization_endpoint": resolveOIDCEndpointURL(cfg.OIDCIssuer, "/authorize/"),
 	})
 }
@@ -840,4 +908,4 @@ func ListenAndServe(ctx context.Context, pool *db.Pool, cfg config.Config) error
 		defer cancel()
 		return srv.Shutdown(shutdownCtx)
 	}
-}
+}

internal/httpapi/skills.go

@@ -0,0 +1,197 @@
+package httpapi
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"log/slog"
+
+	"github.com/dtoro/oikos/internal/db/sqlcgen"
+	"github.com/dtoro/oikos/internal/domain"
+	"github.com/dtoro/oikos/internal/httpapi/gen"
+	"github.com/dtoro/oikos/internal/observability"
+	"github.com/google/uuid"
+	"github.com/jackc/pgx/v5"
+)
+
+// ─── Skills ────────────────────────────────────────────────────────────
+
+func (s *Server) ListSkills(ctx context.Context, req gen.ListSkillsRequestObject) (gen.ListSkillsResponseObject, error) {
+	limit := clampLimit(req.Params.Limit)
+	rows, err := s.pool.Query(ctx, `
+		SELECT s.entity_id, s.version, s.name, s.procedure, s.applies_type,
+		       s.action, s.pattern_ids, s.status, s.success_rate,
+		       s.changed_by::text, s.change_reason, s.last_used_at
+		FROM skills s
+		WHERE ($1::text IS NULL OR s.status = $1)
+		  AND ($2::text IS NULL OR s.applies_type = $2)
+		  AND ($3::text IS NULL OR s.action = $3)
+		ORDER BY s.name, s.version DESC`,
+		req.Params.Status, req.Params.AppliesTo, req.Params.Action)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	// Deduplicate to latest version per skill (the ORDER BY name, version DESC
+	// means the first row per name is the latest).
+	seen := map[string]bool{}
+	items := []gen.Skill{}
+	for rows.Next() {
+		var s gen.Skill
+		var procBytes []byte
+		var patternIDs []uuid.UUID
+		if err := rows.Scan(&s.Id, &s.Version, &s.Name, &procBytes, &s.AppliesType,
+			&s.Action, &patternIDs, &s.Status, &s.SuccessRate,
+			&s.ChangedBy, &s.ChangeReason, &s.LastUsedAt); err != nil {
+			return nil, err
+		}
+		if seen[s.Id.String()] {
+			continue
+		}
+		seen[s.Id.String()] = true
+		if err := json.Unmarshal(procBytes, &s.Procedure); err != nil {
+			slog.Warn("phase3: unmarshal skill procedure", "skill", s.Name, "error", err)
+		}
+		if len(patternIDs) > 0 {
+			pids := make([]string, len(patternIDs))
+			for i, pid := range patternIDs {
+				pids[i] = pid.String()
+			}
+			s.PatternIds = &pids
+		}
+		items = append(items, s)
+		if len(items) > limit {
+			break
+		}
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+
+	if items == nil {
+		items = []gen.Skill{}
+	}
+	return gen.ListSkills200JSONResponse{Items: items}, nil
+}
+
+func (s *Server) PatchSkill(ctx context.Context, req gen.PatchSkillRequestObject) (gen.PatchSkillResponseObject, error) {
+	if req.Body == nil {
+		return nil, fmt.Errorf("%w: request body is required", domain.ErrInvalidInput)
+	}
+
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	tx, err := s.pool.Begin(ctx)
+	if err != nil {
+		return nil, err
+	}
+	defer tx.Rollback(ctx)
+	q := sqlcgen.New(tx)
+
+	if req.Body.Status != nil {
+		if err := q.UpdateSkillStatus(ctx, sqlcgen.UpdateSkillStatusParams{
+			EntityID: id,
+			Status:   string(*req.Body.Status),
+		}); err != nil {
+			if err == pgx.ErrNoRows {
+				return nil, fmt.Errorf("%w: skill %s", domain.ErrNotFound, req.Id)
+			}
+			return nil, err
+		}
+	}
+
+	// Re-read skill.
+	var skill gen.Skill
+	var procBytes []byte
+	var patternIDs []uuid.UUID
+	err = tx.QueryRow(ctx, `
+		SELECT entity_id, version, name, procedure, applies_type, action,
+		       pattern_ids, status, success_rate, changed_by::text,
+		       change_reason, last_used_at
+		FROM skills WHERE entity_id = $1 ORDER BY version DESC LIMIT 1`, id).
+		Scan(&skill.Id, &skill.Version, &skill.Name, &procBytes, &skill.AppliesType,
+			&skill.Action, &patternIDs, &skill.Status, &skill.SuccessRate,
+			&skill.ChangedBy, &skill.ChangeReason, &skill.LastUsedAt)
+	if err != nil {
+		if err == pgx.ErrNoRows {
+			return nil, fmt.Errorf("%w: skill %s", domain.ErrNotFound, req.Id)
+		}
+		return nil, err
+	}
+	if err := json.Unmarshal(procBytes, &skill.Procedure); err != nil {
+			slog.Warn("phase3: unmarshal skill proc", "error", err)
+		}
+	if len(patternIDs) > 0 {
+		pids := make([]string, len(patternIDs))
+		for i, pid := range patternIDs {
+			pids[i] = pid.String()
+		}
+		skill.PatternIds = &pids
+	}
+
+	actorType, actor := actorInfo(ctx)
+	if auditErr := observability.Audit(ctx, q, actorType, actor, "patch",
+		&id, "PATCH", "/api/v1/skills/"+req.Id, "",
+		nil,
+		map[string]any{"status": req.Body.Status, "pinned_version": req.Body.PinnedVersion}); auditErr != nil {
+		return nil, auditErr
+	}
+
+	if err := tx.Commit(ctx); err != nil {
+		return nil, err
+	}
+
+	return gen.PatchSkill200JSONResponse(skill), nil
+}
+
+func (s *Server) ListSkillVersions(ctx context.Context, req gen.ListSkillVersionsRequestObject) (gen.ListSkillVersionsResponseObject, error) {
+	id, err := s.resolveEntityID(ctx, req.Id)
+	if err != nil {
+		return nil, err
+	}
+
+	rows, err := s.pool.Query(ctx, `
+		SELECT entity_id, version, name, procedure, applies_type, action,
+		       pattern_ids, status, success_rate, changed_by::text,
+		       change_reason, last_used_at
+		FROM skills WHERE entity_id = $1
+		ORDER BY version DESC`, id)
+	if err != nil {
+		return nil, err
+	}
+	defer rows.Close()
+
+	items := []gen.Skill{}
+	for rows.Next() {
+		var skill gen.Skill
+		var procBytes []byte
+		var patternIDs []uuid.UUID
+		if err := rows.Scan(&skill.Id, &skill.Version, &skill.Name, &procBytes, &skill.AppliesType,
+			&skill.Action, &patternIDs, &skill.Status, &skill.SuccessRate,
+			&skill.ChangedBy, &skill.ChangeReason, &skill.LastUsedAt); err != nil {
+			return nil, err
+		}
+		if err := json.Unmarshal(procBytes, &skill.Procedure); err != nil {
+			slog.Warn("phase3: unmarshal skill proc", "error", err)
+		}
+		if len(patternIDs) > 0 {
+			pids := make([]string, len(patternIDs))
+			for i, pid := range patternIDs {
+				pids[i] = pid.String()
+			}
+			skill.PatternIds = &pids
+		}
+		items = append(items, skill)
+	}
+	if rows.Err() != nil {
+		return nil, rows.Err()
+	}
+	if items == nil {
+		items = []gen.Skill{}
+	}
+	return gen.ListSkillVersions200JSONResponse{Items: items}, nil
+}

internal/httpapi/stubs.go

@@ -1,6 +0,0 @@
-package httpapi
-
-// Remaining stubs for endpoints that depend on tables not yet created
-// (knowledge_entities, agent_activity). These are kept here because the
-// phase3.go file already defines them; this file is deliberately empty.
-// The stubs live in phase3.go as simple errNotImplemented returns.

internal/knowledge/seed_test.go

@@ -0,0 +1,155 @@
+package knowledge
+
+import (
+	"crypto/sha256"
+	"encoding/hex"
+	"reflect"
+	"testing"
+)
+
+func TestContentHash(t *testing.T) {
+	t.Run("determinism", func(t *testing.T) {
+		a := contentHash("hello")
+		b := contentHash("hello")
+		if a != b {
+			t.Errorf("contentHash not deterministic: %q != %q", a, b)
+		}
+	})
+
+	t.Run("empty string known sha256", func(t *testing.T) {
+		got := contentHash("")
+		h := sha256.Sum256([]byte(""))
+		want := hex.EncodeToString(h[:])
+		if got != want {
+			t.Errorf("contentHash(\"\") = %q, want %q", got, want)
+		}
+	})
+
+	t.Run("different inputs different outputs", func(t *testing.T) {
+		if contentHash("a") == contentHash("b") {
+			t.Error("different inputs produced same hash")
+		}
+	})
+
+	t.Run("output is 64-char hex", func(t *testing.T) {
+		got := contentHash("anything")
+		if len(got) != 64 {
+			t.Errorf("len = %d, want 64", len(got))
+		}
+		for _, r := range got {
+			isHex := (r >= '0' && r <= '9') || (r >= 'a' && r <= 'f')
+			if !isHex {
+				t.Errorf("non-hex char %q in hash %q", r, got)
+				break
+			}
+		}
+	})
+}
+
+func TestStr(t *testing.T) {
+	cases := []struct {
+		name string
+		m    map[string]any
+		key  string
+		want string
+	}{
+		{"missing key", map[string]any{}, "nope", ""},
+		{"string value", map[string]any{"k": "v"}, "k", "v"},
+		{"int value", map[string]any{"k": 42}, "k", ""},
+		{"nil value", map[string]any{"k": nil}, "k", ""},
+		{"empty string", map[string]any{"k": ""}, "k", ""},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			got := str(c.m, c.key)
+			if got != c.want {
+				t.Errorf("str() = %q, want %q", got, c.want)
+			}
+		})
+	}
+}
+
+func TestStrSlice(t *testing.T) {
+	cases := []struct {
+		name string
+		m    map[string]any
+		key  string
+		want []string
+	}{
+		{"missing key", map[string]any{}, "tags", nil},
+		{"all strings", map[string]any{"tags": []any{"a", "b", "c"}}, "tags", []string{"a", "b", "c"}},
+		{"mixed types", map[string]any{"tags": []any{1, "a", true, "b"}}, "tags", []string{"a", "b"}},
+		{"empty array", map[string]any{"tags": []any{}}, "tags", []string{}},
+		{"nil elements filtered", map[string]any{"tags": []any{nil, "a", nil, "b"}}, "tags", []string{"a", "b"}},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			got := strSlice(c.m, c.key)
+			if len(got) != len(c.want) {
+				t.Errorf("len = %d, want %d (got %v)", len(got), len(c.want), got)
+				return
+			}
+			for i := range got {
+				if got[i] != c.want[i] {
+					t.Errorf("[%d] = %q, want %q", i, got[i], c.want[i])
+				}
+			}
+		})
+	}
+}
+
+func TestMapVal(t *testing.T) {
+	cases := []struct {
+		name string
+		m    map[string]any
+		key  string
+		want map[string]any
+	}{
+		{"missing key", map[string]any{}, "nope", nil},
+		{"present map", map[string]any{"k": map[string]any{"x": 1}}, "k", map[string]any{"x": 1}},
+		{"wrong type string", map[string]any{"k": "v"}, "k", nil},
+		{"nested map", map[string]any{"k": map[string]any{"a": map[string]any{"b": 2}}}, "k", map[string]any{"a": map[string]any{"b": 2}}},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			got := mapVal(c.m, c.key)
+			if !reflect.DeepEqual(got, c.want) {
+				t.Errorf("mapVal() = %v, want %v", got, c.want)
+			}
+		})
+	}
+}
+
+func TestToPGArray(t *testing.T) {
+	cases := []struct {
+		name string
+		tags []string
+		want string
+	}{
+		{"empty", []string{}, "{}"},
+		{"single", []string{"a"}, `{"a"}`},
+		{"multiple", []string{"a", "b"}, `{"a","b"}`},
+		{"nil", nil, "{}"},
+	}
+	for _, c := range cases {
+		t.Run(c.name, func(t *testing.T) {
+			got := toPGArray(c.tags)
+			if got != c.want {
+				t.Errorf("toPGArray() = %q, want %q", got, c.want)
+			}
+		})
+	}
+
+	// Special chars: tags containing " or \ are NOT escaped by toPGArray.
+	// This is a latent bug — Postgres array literals require these to be
+	// backslash-escaped. Test documents current behavior so a fix is
+	// detectable. Should be fixed.
+	t.Run("special chars unescaped (current buggy behavior)", func(t *testing.T) {
+		got := toPGArray([]string{`a"b`, `c\d`})
+		// Current output: {"a"b","c\d"} — invalid Postgres array literal.
+		want := `{"a"b","c\d"}`
+		if got != want {
+			t.Errorf("toPGArray(special) = %q, want %q (if this changed, the escaping bug was fixed — update this test)", got, want)
+		}
+	})
+}

internal/learning/learning.go

@@ -83,27 +83,13 @@ func extractPatterns(ctx context.Context, pool *db.Pool, watermark time.Time) ti
 func processGroup(ctx context.Context, pool *db.Pool, q *sqlcgen.Queries,
 	appliesType, action string, items []sqlcgen.GetFeedbackAfterWatermarkRow) {
 
-	successCount := 0
-	failureCount := 0
-	for _, f := range items {
-		switch f.Outcome {
-		case "success":
-			successCount++
-		case "failure", "unexpected":
-			failureCount++
-		case "partial":
-			successCount++ // partial counts as half-success
-		}
-	}
+	successCount, failureCount := countOutcomes(items)
 	total := successCount + failureCount
 	if total == 0 {
 		return
 	}
 
-	// Compute Wilson score lower bound
-	confidence := wilsonLowerBound(float64(successCount), float64(total), 0.95)
-	// Cap by sample size: nothing looks confident before 5 samples
-	confidence = math.Min(confidence, float64(total)/5.0)
+	confidence := computeConfidence(successCount, failureCount)
 
 	// Get or create pattern — first look up existing entity, then upsert.
 	existing, err := q.GetPattern(ctx, sqlcgen.GetPatternParams{
@@ -148,7 +134,7 @@ func processGroup(ctx context.Context, pool *db.Pool, q *sqlcgen.Queries,
 		return
 	}
 
-	if pat.EvidenceCount >= 5 && pat.Confidence >= 0.7 && !pat.Quarantined {
+	if shouldValidate(int(pat.EvidenceCount), float64(pat.Confidence), pat.Quarantined) {
 		_ = q.UpdatePatternStatus(ctx, sqlcgen.UpdatePatternStatusParams{
 			EntityID: pat.EntityID,
 			Status:   "validated",
@@ -158,8 +144,7 @@ func processGroup(ctx context.Context, pool *db.Pool, q *sqlcgen.Queries,
 			"confidence", confidence, "samples", total)
 	}
 
-	// Anomaly check: >10 identical outcomes within 1h
-	if total > 10 {
+	if shouldQuarantine(total) {
 		_ = q.UpdatePatternQuarantine(ctx, sqlcgen.UpdatePatternQuarantineParams{
 			EntityID:    pat.EntityID,
 			Quarantined: true,
@@ -169,6 +154,45 @@ func processGroup(ctx context.Context, pool *db.Pool, q *sqlcgen.Queries,
 	}
 }
 
+// countOutcomes tallies feedback items into success and failure counts.
+// "partial" counts as a half-success (increments success).
+func countOutcomes(items []sqlcgen.GetFeedbackAfterWatermarkRow) (success, failure int) {
+	for _, f := range items {
+		switch f.Outcome {
+		case "success":
+			success++
+		case "failure", "unexpected":
+			failure++
+		case "partial":
+			success++
+		}
+	}
+	return success, failure
+}
+
+// computeConfidence calculates the Wilson score lower bound, capped by
+// sample size (nothing looks confident before 5 samples).
+func computeConfidence(success, failure int) float64 {
+	total := success + failure
+	if total == 0 {
+		return 0
+	}
+	confidence := wilsonLowerBound(float64(success), float64(total), 0.95)
+	return math.Min(confidence, float64(total)/5.0)
+}
+
+// shouldValidate returns true when a pattern has enough evidence and
+// confidence to be promoted from "hypothesized" to "validated".
+func shouldValidate(evidenceCount int, confidence float64, quarantined bool) bool {
+	return evidenceCount >= 5 && confidence >= 0.7 && !quarantined
+}
+
+// shouldQuarantine returns true when an anomaly burst is detected
+// (>10 identical outcomes, indicating a runaway loop rather than organic feedback).
+func shouldQuarantine(total int) bool {
+	return total > 10
+}
+
 // wilsonLowerBound computes the Wilson score interval lower bound.
 // Conservative estimate of success rate for small sample sizes.
 func wilsonLowerBound(success, total, z float64) float64 {