docs(R5): rewrite knowledge schema + llm-wiki for DB-native model; deprecate root inventory.yaml

Rewrote .agents/domains/knowledge/schema.md and .agents/shared/llm-wiki.md
which described the deleted Python substrate (bin/homelab, oikos/cards/,
oikos/ledger.py, root inventory.yaml, knowledge/sources/, get_page/
search_docs MCP tools). Now reflect ADR 0003: Postgres DB is the single
source of truth for structured data and narrative knowledge; seeds/*.yaml
are bootstrap+DR manifests (content-hashed via seed_versions); archive/
knowledge/ is the frozen legacy wiki; MCP search_knowledge/get_entity_
knowledge replace get_page/search_docs.

Swept substrate refs in .agents/shared/{writing-style,page-templates}.md
and .agents/domains/operations/schema.md: bare inventory.yaml ->
seeds/inventory.yaml; knowledge/sources/ -> archive/knowledge/sources/
(historical); get_changelog/oikos/ledger.py -> DB audit trail / structured
document changelog field; HERMES -> Nomos.

Root inventory.yaml (618-line Python-era file superseded 2026-07-07 by
seeds/inventory.yaml) replaced with a deprecation stub pointing to the seed
and DB. Kept as a stub rather than deleted because AGENTS.md §1/§2 still
point clients at /opt/homelab-context/inventory.yaml; full on-client path
reconciliation deferred to R13.

Flagged export gap: oikos export regenerates seeds/{ontology,inventory,
policy}.yaml but NOT seeds/knowledge.yaml — API-added knowledge lives only
in the DB until hand-edited into the seed.

VERSION 0.7.7 -> 0.7.8. Plan R5 marked done.

.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
+The knowledge domain is the durable, authoritative current-state documentation of the homelab:
-page per node and per cross-cutting system, synthesized from live state and evidence. It answers
+narrative for every node and cross-cutting system, synthesized from live state and evidence. It
-"what exists and how does it work right now."
+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
+Per ADR 0003, the Postgres database is the single source of truth for all structured data **and**
-describes but never contains. The split is load-bearing: several programs read the substrate at
+narrative knowledge. The narrative/substrate split of the Python era is gone: the DB holds both the
-fixed paths, so the wiki reorganization never moves it.
+structured graph (entities, relationships, status, metrics) and the narrative layer (documents,
+investigations, runbooks) in the `knowledge_entities` table.
 
-| Layer | Location | Consumed by |
+| Concern | Where it lives | How it gets there |
-|-------|----------|-------------|
+|---------|----------------|-------------------|
-| Substrate — source of truth | `inventory.yaml` (root) | MCP server, `homelab` CLI, `oikos/` scheduler/drift/relations/gen-topology |
+| 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 |
-| Substrate — generated host records | `inventory.yaml` (root) | Go `internal/mcp/` server, `bin/homelab`; the single source of truth |
+| Seed manifest (bootstrap + DR) | `seeds/knowledge.yaml` | Hand-edited or regenerated; ingested idempotently (content-hashed via `seed_versions`) |
-| Substrate — kernel + context cards | `oikos/` (code, `oikos/cards/`, `oikos/state.json`) | MCP `explain`, scheduler |
+| Structured graph — hosts, services, entity types, relationships | `entities`, `relationships`, `entity_types` tables | Seeded from `seeds/{ontology,inventory}.yaml`; mutated via API/MCP |
-| Narrative — synthesized wiki | `archive/knowledge/{hosts,containers,vms,infrastructure}/` | humans, agents via MCP `get_page` / `search_docs` |
+| Archived narrative wiki (read-only history) | `archive/knowledge/` | Frozen 2026-07-07 when the DB became source of truth |
-| Evidence — immutable sources | `knowledge/sources/` (references + investigations) | synthesis into wiki pages |
 
-## Wiki pages
+### Seed ingest
 
-- **Node pages** (`archive/knowledge/containers/<id>-<name>.md`, `.../vms/<id>-<name>.md`,
+`seeds/knowledge.yaml` has three top-level lists — `documents`, `investigations`, `runbooks` — each
-  `.../hosts/<name>.md`) follow the container/host template in
+entry carrying `slug`, `title`, `content` (markdown), and tags. `internal/knowledge/seed.go`
-  [page-templates.md](../../shared/page-templates.md): opening definition, `## At a glance`,
+ingests each entry by:
-  `## Role`, service/port map, storage, auto-deploy, `## Related`, `## Changelog`.
+
-- **Cross-cutting pages** (`archive/knowledge/infrastructure/<topic>.md`) follow the cross-cutting
+1. `getOrCreateEntity` — ensures the slug exists in `entities` (type `document` / `investigation` /
-  template: `## Why`, `## Components`, `## How to apply`, `## Gotchas`, `## Related`, `## Changelog`.
+   `runbook`).
-- Each `inventory.yaml` host entry carries a `doc_page:` field pointing at its narrative page.
+2. `upsertKnowledgeEntity` — writes the markdown body into `knowledge_entities`, keyed by
-  Changing where a page lives means updating that field (read by `bin/homelab`).
+   `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
+- The per-document **`## Changelog`** records infrastructure changes to that node. Keep the
-  (`get_changelog`, the Oikos ledger). Keep the `### YYYY-MM-DD — title` shape.
+  `### YYYY-MM-DD — title` shape so the parsed `changelog` field stays structured.
-- **`knowledge/log.md`** is append-only and records *documentation-maintenance* operations only
+- **`archive/knowledge/log.md`** is the append-only record of *documentation-maintenance*
-  (restructures, source ingests, lint sweeps): `## [YYYY-MM-DD] <op> | <summary>`. It never
+  operations on the legacy wiki (restructures, source ingests, lint sweeps):
-  duplicates the Oikos change ledger (`oikos/ledger.py`).
+  `## [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
+A change to a node updates the DB in the same session — the entity's attributes, the relationships
-section `README.md` table, the root `README.md`, the Caddy/DNS/ingress pages, the host page, and
+that reference it, and any document whose `at_glance` or changelog should reflect the new state. See
-`inventory.yaml`. See [page-templates.md](../../shared/page-templates.md#same-session-update-rule).
+[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
+reference (command cheatsheet, enrollment, Nomos agent) lives in
-[`.agents/operations/`](../../operations/); investigations are sources under
+[`.agents/operations/`](../../operations/); investigations are `investigation` entities in the DB
-`knowledge/sources/investigations/`; plans stay in the repo-root `plans/` folder (below).
+(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
+Incident records are `investigation` entities in the DB, linked to the entities they implicate via
-once at incident time, then linked from the changelogs of the nodes they implicate. Sections:
+`about` edges. They are **evidence sources** — written once at incident time, then back-linked from
-`## Summary`, `## Timeline`, `## Root cause`, `## Mitigations applied`, `## Open questions`. Resolved
+the changelogs of the nodes they implicate. Sections: `## Summary`, `## Timeline`, `## Root cause`,
-incidents move to `knowledge/sources/investigations/archive/`.
+`## 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
+`plans/log.md` is the append-only record of documentation operations on plans
-those areas (`## [YYYY-MM-DD] <op> | <summary>`), distinct from the Oikos change ledger.
+(`## [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/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
+How documentation in this repo is organized. The pattern is the `sources / wiki / index / log`
-`sources / wiki / index / log` model: a durable synthesized layer (`archive/knowledge/`) built on top
+model: a durable synthesized layer built on top of immutable evidence, with pure-listing indexes and
-of immutable evidence (`knowledge/sources/`, incident records), with pure-listing indexes and an
+an append-only operations log.
-append-only operations log.
 
-This contract governs the **narrative layer only**. The machine-readable substrate — `inventory.yaml`,
+This contract governs the **narrative layer only**. The machine-readable source of truth — the
-`secrets/`, `scripts/`, `bin/` — is not part of the wiki and never
+Postgres database, bootstrapped from `seeds/` — is not part of the wiki and never moves under it.
-moves under it. See [the knowledge schema](../domains/knowledge/schema.md) for the split.
+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
+- **Source of truth** is the Postgres database. Structured data (entities, relationships, status,
-  docs (`knowledge/sources/references/`), and the live system itself (`pct config`, `docker inspect`).
+  metrics) and narrative knowledge (documents, investigations, runbooks) both live there, in the
-  Read them; do not rewrite them into other sources.
+  `entities` / `relationships` / `knowledge_entities` tables. It is bootstrapped at deploy time from
-- **Wiki** (`archive/knowledge/`) is the synthesized, authoritative current-state layer: one page per
+  `seeds/{ontology,inventory,policy,knowledge}.yaml` (idempotent, content-hashed via
-  node (`containers/`, `vms/`, host narratives) and per cross-cutting system (`infrastructure/`). A
+  `seed_versions`) and mutated at runtime via the API/MCP. `oikos export` regenerates
-  reader understands the topic from the wiki page without reading the sources.
+  `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
+- **Log** is append-only, recording *doc-maintenance operations* (restructures, source ingests,
-  ingests, lint sweeps) in single-line format: `## [YYYY-MM-DD] <op> | <summary>`.
+  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
+- **`## Changelog`** on each node/topic document records *infrastructure* changes to that node. It
-  machine-parsed (`get_changelog`, the Oikos ledger) — keep the `### YYYY-MM-DD — title` shape.
+  is stored as a structured field on the `document` entity — keep the `### YYYY-MM-DD — title`
-- **`log.md`** per area records *documentation* operations only. It never duplicates the Oikos
+  shape so it parses cleanly.
-  change ledger (`oikos/ledger.py`), which stays authoritative for infra changes with
+- **Doc-maintenance logs** record *documentation* operations only. They never duplicate the
-  who/what/risk/approval/verification.
+  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

@@ -14,7 +14,7 @@ in [writing-style.md](writing-style.md); the layer model (sources / wiki / index
 
 **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
+mount, deploy a new service — **update the DB and every relevant doc page in
-session.** A change that touches a container page must also update:
+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

VERSION

@@ -1 +1 @@
-0.7.7
+0.7.8

inventory.yaml

@@ -1,618 +1,28 @@
-# Homelab inventory — canonical structured topology.
+# DEPRECATED — 2026-07-17 (R5). Do not edit. Do not consume.
 #
-# Single source of truth. hosts/*.yaml is generated from this file by
+# This root-level inventory.yaml is the Python-era topology file. It was
-# mcp/build_host_files.py; do NOT edit those by hand.
+# superseded on 2026-07-07 by the DB-native model (ADR 0003):
 #
-# Conventions:
+#   - The Postgres database is the single source of truth for all structured
-#   - hostname keys MUST match the actual `hostname` of the machine (on
+#     data. Query it via MCP `get_entity` / `list_entities` or the REST API.
-#     macOS: `scutil --get LocalHostName` if set).
+#   - `seeds/inventory.yaml` is the bootstrap + DR seed manifest, ingested
-#   - `os:` one of: linux, macos
+#     idempotently into the DB at deploy time (content-hashed via
-#   - `kind:` one of: proxmox-host, lxc, vm, workstation, external
+#     `seed_versions`). `oikos export` regenerates it from the DB for VC.
-#     ("external" is reserved for hosts the homelab CLI manages via ssh but
+#   - `archive/knowledge/` holds the frozen legacy narrative wiki.
-#      that aren't homelab clients themselves — e.g. the IONOS netbird VPS
-#      with no /etc/age/key.txt and no /opt/homelab-context clone.)
-#   - `mesh:` lists addresses the host is reachable at. Both `netbird` and
-#     `tailscale` are accepted during the migration (see infrastructure/mesh.md).
-#     Prefer netbird FQDNs over raw IPs.
-#   - `age_pubkey:` provisioned by secrets-issuance on first bootstrap and
-#     committed back via `homelab client add --finalize-pubkey <key>`.
-#   - When a service moves hosts, update only the `services:` section here;
-#     never duplicate addresses elsewhere.
-#   - `ssh.user:` per-host login user. Default is `root` if omitted (matches
-#     every LXC + the PVE host). Set explicitly for workstations whose login
-#     user differs from `root`. Used by the `homelab` CLI to build
-#     `user@host` and to inform anyone running raw `netbird ssh` (which
-#     defaults to the LOCAL username — the gotcha that creates "user not
-#     found" errors when ssh'ing INTO machines that only have `root`).
 #
-# `homelab client add/remove` does surgical line-edits — comments survive.
+# This file is kept only because AGENTS.md §1/§2 still point clients at
-# Avoid round-tripping the file through yaml.safe_dump (it strips comments).
+# `/opt/homelab-context/inventory.yaml` (the on-client clone path). Reconcile
-
+# that path to `seeds/inventory.yaml` and delete this stub — tracked as R13
-mesh:
+# in plans/2026-07-17-codebase-review-and-cleanup.md.
-  primary: netbird
+#
-  accepted:
+# The live topology is in the DB. The seed is `seeds/inventory.yaml`. This
-  - netbird
+# file is not read by any Go code, script, or test in the repo.
-  - tailscale
+---
-  netbird_subnet: 100.122.0.0/16
+deprecated: true
-  netbird_domain: netbird.selfhosted
+superseded_by: seeds/inventory.yaml
-# Service contract (Oikos, 2026-07-05): each service should carry
+source_of_truth: postgres (see ADR 0003)
-#   backend        host/container that runs it (required)
+see_also:
-#   url            public URL if ingress-exposed
+  - seeds/inventory.yaml
-#   doc_page       owning wiki page
+  - seeds/ontology.yaml
-#   config_repo    tracked config repo, if any (mutations go commit+push)
+  - seeds/policy.yaml
-#   health         health-check URL if it differs from `url`
+  - docs/adr/0003-db-native-ontology-yaml-seeds.md
-#   risk_notes     what an agent must know before touching it
-# See oikos/ontology.yaml + oikos/policy.yaml.
-services:
-  proxmox_ui:
-    url: https://proxmox.hubris.network
-    backend: hubris
-    port: 8006
-    doc_page: knowledge/wiki/hosts/hubris.md
-    risk_notes: hypervisor UI — changes here affect every guest on the node
-  gitea:
-    url: https://git.hubris.network
-    backend: gitea
-    backend_url: http://192.168.8.121:3000
-    doc_page: knowledge/wiki/containers/104-gitea.md
-    config_repo: dtoro/gitea-customizations
-    risk_notes: hosts all config repos + deploy webhooks; outage blocks auto-deploy and sync
-  caddy:
-    backend: caddy
-    role: reverse-proxy
-    note: terminates all *.hubris.network
-    doc_page: knowledge/wiki/containers/121-caddy.md
-    config_repo: dtoro/caddy-conf
-    risk_notes: wide blast radius — every *.hubris.network route rides on it (see oikos/policy.yaml service_overrides)
-  authentik:
-    url: https://auth.hubris.network
-    backend: netbird-vps
-    doc_page: knowledge/wiki/containers/106-auth-outpost.md
-    note: >-
-      core runs on the VPS since 2026-05-31; LAN forward-auth outpost is
-      auth-outpost (LXC 106) at 192.168.8.6:9000. Previous backend value
-      "authentik" referenced the retired embedded-outpost host (LXC 124).
-    risk_notes: SSO provider — outage locks login to OIDC/forward-auth services
-  dns:
-    backend: dns
-    note: Technitium DNS, split-horizon zone
-    doc_page: knowledge/wiki/containers/107-dns.md
-    risk_notes: LAN-wide resolver — misconfig breaks name resolution for every client
-  jellyfin:
-    url: https://media.hubris.network
-    backend: jellyfin
-    doc_page: knowledge/wiki/containers/101-jellyfin.md
-    risk_notes: native Authentik OIDC via SSO-Auth plugin, no Caddy forward-auth gate; VAAPI transcode depends on GPU passthrough on strong
-  nextcloud:
-    url: https://cloud.hubris.network
-    backend: nextcloud
-    doc_page: knowledge/wiki/containers/114-nextcloud.md
-  paperless:
-    url: https://paperless.hubris.network
-    backend: paperless
-    doc_page: knowledge/wiki/containers/103-paperless.md
-    risk_notes: document archive — treat data as irreplaceable; DB operations are destructive-class
-  matrix:
-    url: https://matrix.hubris.network
-    backend: elementsynapse
-    doc_page: knowledge/wiki/containers/118-elementsynapse.md
-    risk_notes: alert/approval channel for Oikos — outage silences agent escalation
-  photos:
-    url: https://photos.hubris.network
-    backend: mule-images
-    doc_page: knowledge/wiki/containers/120-mule-images.md
-    config_repo: dtoro/mule-image
-  arr_stack:
-    backend: arriman
-    note: jellyseerr / qbit / sab on docker compose
-    doc_page: knowledge/wiki/containers/122-arriman.md
-  artifacto:
-    backend: apps
-    url: https://artifacto.hubris.network
-    doc_page: knowledge/wiki/containers/105-apps.md
-    config_repo: dtoro/Artifacto
-  trmnl:
-    backend: trmnl
-    url: https://trmnl.hubris.network
-    note: self-hosted middleware for TRMNL e-ink plugins (polled by TRMNL cloud)
-    doc_page: knowledge/wiki/containers/128-trmnl.md
-    config_repo: dtoro/terminalito
-  zimaos:
-    url: https://zimaos.hubris.network
-    backend: zimaos
-    doc_page: knowledge/wiki/vms/100-zimaos.md
-  haos:
-    backend: haos
-    doc_page: knowledge/wiki/vms/108-haos.md
-  teddycloud:
-    url: https://teddy.hubris.network
-    backend: teddycloud
-    doc_page: knowledge/wiki/containers/131-teddycloud.md
-    note: self-hosted TeddyCloud (Toniebox cloud reimplementation), docker compose
-    risk_notes: no Caddy forward-auth gate (unlike sab.hubris.network on the same Caddyfile) —
-      reachable to anyone on the LAN/mesh who can resolve teddy.hubris.network; undocumented
-      in inventory.yaml until 2026-07-06 (drift-caught)
-  homelab_mcp:
-    backend: apps
-    port: 9810
-    systemd_unit: homelab-mcp
-    public_host: mcp.hubris.network
-    endpoint: https://mcp.hubris.network/mcp
-    doc_page: knowledge/wiki/infrastructure/homelab-context.md
-    config_repo: dtoro/oikos
-    note: MCP server. Read-only context + management. Reachable on the LAN via Caddy
-      and from off-LAN via Netbird (192.168.8.0/24 is a network resource routed through
-      hubris).
-    risk_notes: agents' primary read surface — outage degrades every agent to grepping the clone
-  secrets_issuance:
-    backend: apps
-    port: 9820
-    systemd_unit: secrets-issuance
-    public_host: secrets.hubris.network
-    endpoint: https://secrets.hubris.network/issue
-    doc_page: .agents/operations/agent-enrollment.md
-    config_repo: dtoro/oikos
-    note: Issues per-client age private keys. Gated at source-IP layer (mesh + LAN
-      subnets in MESH_SUBNETS).
-    risk_notes: identity issuance — any change is security-sensitive; key operations are destructive-class
-hosts:
-  hubris:
-    kind: proxmox-host
-    os: linux
-    role: hypervisor
-    lan_ip: 192.168.8.77
-    mesh:
-      netbird:
-        ip: 100.122.38.109
-        fqdn: proxmox-server.netbird.selfhosted
-    ssh:
-      port: 22
-      netbird_port: 22022
-      user: root
-    mounts:
-    - /mnt/library
-    age_pubkey: age1xkklkvnk5z0fsnh6cfgv70hy9ksfy8rdprwerzw4yk3p4p7cxcqs2yvpz6
-  trmnl:
-    kind: lxc
-    pve_id: 128
-    host: hubris
-    os: linux
-    role: trmnl-middleware
-    lan_ip: 192.168.8.211
-    public_host: trmnl.hubris.network
-    # not yet mesh/SOPS-enrolled — see containers/128-trmnl.md
-  house:
-    kind: lxc
-    pve_id: 129
-    host: strong
-    os: linux
-    role: family-planner
-    lan_ip: 192.168.8.244
-    public_host: house.hubris.network
-    notes:
-    - Docker host for Yuvomi (family planner). Created 2026-06-26.
-    - Migrated from hubris to strong 2026-07-05 (Phase 1 of strong migration plan).
-    - Runs Yuvomi container + WebDAV doc bridge to paperless
-    - 192.168.8.212 was the hubris IP before migration (briefly picked up by teddycloud via
-      DHCP; teddycloud has since been given a static IP, see hosts.teddycloud)
-    age_pubkey: age1s07zs83ehtlg8jtwvr75ltc3c4cdlemfwjuxrwjtwkqxkl9tpggsyrzn2h
-  jellyfin:
-    kind: lxc
-    pve_id: 101
-    host: strong
-    os: linux
-    role: media-server
-    lan_ip: 192.168.8.246
-    public_host: media.hubris.network
-    mesh:
-      tailscale:
-        fqdn: jellyfin
-    mounts:
-    - /mnt/media_local
-    notes:
-    - Jellyfin 10.11.11 with VAAPI hardware acceleration (Radeon 680M iGPU on strong)
-    - 4 cores / 8 GiB RAM / 1 GiB swap
-    - SSO-Auth plugin v4.0.0.4 with Authentik OIDC (no Caddy forward-auth gate)
-    - GPU passed via dev0+dev1: /dev/dri/renderD128 + card0
-    - Migrated from hubris to strong 2026-07-05 (Phase 2). Library on ludo-lvm.
-    age_pubkey: ''
-  nfs-export:
-    kind: lxc
-    pve_id: 102
-    host: hubris
-    os: linux
-    role: storage-export
-    lan_ip: 192.168.8.200
-  paperless:
-    kind: lxc
-    pve_id: 103
-    host: hubris
-    os: linux
-    role: document-archive
-    lan_ip: 192.168.8.130
-    public_host: paperless.hubris.network
-    mesh:
-      tailscale:
-        fqdn: paperless
-    mounts:
-    - /mnt/library
-    age_pubkey: ''
-  gitea:
-    kind: lxc
-    pve_id: 104
-    host: hubris
-    os: linux
-    role: git-server
-    lan_ip: 192.168.8.121
-    public_host: git.hubris.network
-    backend_port: 3000
-    mesh:
-      tailscale:
-        fqdn: gitea
-    mounts:
-    - /mnt/library
-    notes:
-    - Bare repos live at /mnt/library/repos/dtoro/*.git
-    age_pubkey: ''
-  apps:
-    kind: lxc
-    pve_id: 105
-    host: hubris
-    os: linux
-    role: docker-apps
-    lan_ip: 192.168.8.205
-    public_hosts:
-    - artifacto.hubris.network
-    mesh:
-      tailscale:
-        ip: 100.121.171.122
-        fqdn: apps
-    mounts:
-    - /mnt/library
-    runs:
-    - artifacto
-    - plantuml
-    - homelab-mcp
-    - secrets-issuance
-    # booklore removed 2026-06-29 → migrated to grimmory (LXC 130)
-    age_pubkey: age1duyl8mkpgu80uv934dy8q7enqjms6yvdz264hme8uryuxmvvqesq6rusq0
-  auth-outpost:
-    kind: lxc
-    pve_id: 106
-    host: hubris
-    os: linux
-    role: authentik-gateway
-    lan_ip: 192.168.8.6
-    notes:
-    - Runs Authentik outpost (reverse-proxy/SSO enforcement) for protected services
-  dns:
-    kind: lxc
-    pve_id: 107
-    host: hubris
-    os: linux
-    role: dns-server
-    lan_ip: 192.168.8.2
-    notes:
-    - Technitium DNS, split-horizon zone for *.hubris.network
-    - Primary DNS for 192.168.8.0/24 LAN (inventory.services.dns references this)
-  nextcloud:
-    kind: lxc
-    pve_id: 114
-    host: hubris
-    os: linux
-    role: file-sync
-    lan_ip: 192.168.8.224
-    public_host: cloud.hubris.network
-    mesh:
-      tailscale:
-        fqdn: nextcloud
-    mounts:
-    - /mnt/library
-    age_pubkey: ''
-  elementsynapse:
-    kind: lxc
-    pve_id: 118
-    host: strong
-    os: linux
-    role: matrix-server
-    lan_ip: 192.168.8.242
-    public_host: matrix.hubris.network
-    mesh:
-      tailscale: {}
-    notes:
-    - Migrated from hubris to strong 2026-07-05 (Phase 1 of strong migration plan).
-  sophia:
-    kind: lxc
-    pve_id: 119
-    host: hubris
-    os: linux
-    role: workshop
-    lan_ip: 192.168.8.109
-    mesh:
-      tailscale:
-        fqdn: sophia
-    mounts:
-    - /mnt/library
-    age_pubkey: ''
-  mule-images:
-    kind: lxc
-    pve_id: 120
-    host: hubris
-    os: linux
-    role: photo-management
-    lan_ip: 192.168.8.136
-    public_host: photos.hubris.network
-    mesh:
-      tailscale:
-        fqdn: muleimage
-    mounts:
-    - /mnt/library
-    age_pubkey: ''
-  caddy:
-    kind: lxc
-    pve_id: 121
-    host: hubris
-    os: linux
-    role: reverse-proxy
-    lan_ip: 192.168.8.175
-    notes:
-    - Terminates all *.hubris.network
-    - /etc/caddy is a git checkout of dtoro/caddy-conf
-    peers:
-    - authentik
-    - gitea
-  arriman:
-    kind: lxc
-    pve_id: 122
-    host: strong
-    os: linux
-    role: arr-stack
-    lan_ip: 192.168.8.245
-    public_hosts:
-    - jellyseerr.hubris.network
-    - qbit.hubris.network
-    - sab.hubris.network
-    mesh:
-      tailscale:
-        fqdn: arr
-    mounts:
-    - /mnt/media_local
-    notes:
-    - Migrated from hubris to strong 2026-07-05 (Phase 2). Library on ludo-lvm.
-    - Contains homarr, radarr, sonarr, lidarr, sabnzbd, qbittorrent, bazarr, flaresolverr, prowlarr, jellyseerr
-    - qBittorrent auth subnet whitelist expanded to 192.168.8.0/24 (for seanime + Caddy access)
-    age_pubkey: ''
-  grimmory:
-    kind: lxc
-    pve_id: 130
-    host: strong
-    os: linux
-    role: book-library
-    lan_ip: 192.168.8.247
-    public_host: books.hubris.network
-    mounts:
-    - /mnt/media_local
-    notes:
-    - Docker host for Grimmory (community fork of Booklore). Created 2026-06-29.
-    - Migrated from hubris to strong 2026-07-05 (Phase 2d). Books on ludo-lvm.
-    age_pubkey: age1uellsemnjrzgfg9fxw4jefpy05laxzggwnwhh6ny3wl7alyp6v8q0muxet
-  teddycloud:
-    kind: lxc
-    pve_id: 131
-    host: hubris
-    os: linux
-    role: teddycloud
-    lan_ip: 192.168.8.150
-    public_host: teddy.hubris.network
-    mounts:
-    - /mnt/library
-    state: active
-    notes:
-    - Docker host for TeddyCloud (ghcr.io/toniebox-reverse-engineering/teddycloud), a
-      self-hosted reimplementation of the Toniebox cloud backend. Debian 12 (bookworm).
-    - 1 core / 1 GiB RAM / 512 MiB swap / 16 GiB rootfs (local-lvm).
-    - Predates the client-enrollment convention — undocumented in inventory.yaml until
-      2026-07-06, when Oikos's drift detector (oikos/drift.py) caught pve_id 131 live on
-      hubris (`pct list`) with no inventory entry. Static IP assigned 2026-07-05 during the
-      strong migration (was picking up 192.168.8.243 via DHCP before that — see
-      hosts/strong.md's 2026-07-05 changelog).
-    - No age_pubkey / homelab-context enrollment — not a homelab CLI client, just a
-      docker-compose app container. Not a required follow-up unless it needs secrets.
-  seanime:
-    kind: lxc
-    pve_id: 133
-    host: strong
-    os: linux
-    role: anime-media-server
-    lan_ip: 192.168.8.248
-    public_host: seanime.hubris.network
-    mounts:
-    - /mnt/media_local/anime
-    notes:
-    - Seanime anime media server for online streaming + local library scanning
-    - Created 2026-07-05. Binary at /opt/seanime/bin/seanime, systemd service.
-    - Connected to qBittorrent on arriman (192.168.8.245:8080)
-    - 8 online streaming extensions installed (HiAnime, AniWatch, KickAssAnime, etc.)
-    - /anime mounted from strong ludo-lvm (/mnt/media_local/anime)
-    - Caddy: https://seanime.hubris.network → 192.168.8.248:43211
-    - qBittorrent auth subnet whitelist expanded to 192.168.8.0/24 for seanime access
-  romm:
-    kind: lxc
-    pve_id: 134
-    host: strong
-    os: linux
-    role: rom-manager
-    lan_ip: 192.168.8.249
-    public_host: roms.hubris.network
-    mounts:
-    - /mnt/media_local
-    notes:
-    - Docker host for RomM (romm.app) self-hosted ROM manager. Created 2026-07-05.
-    - MariaDB sidecar at /opt/romm/docker-compose.yml.
-    - ROMs on ludo-lvm media volume at /mnt/media_local/roms.
-    - 1 core / 2 GiB RAM / 16 GiB rootfs (ludo-lvm).
-  zimaos:
-    kind: vm
-    pve_id: 100
-    host: hubris
-    os: linux
-    role: nas-frontend-eval
-    lan_ip: 192.168.8.195
-    public_host: zimaos.hubris.network
-  haos:
-    kind: vm
-    pve_id: 108
-    host: hubris
-    os: linux
-    role: home-automation
-    lan_ip: 192.168.8.101
-    mesh:
-      tailscale:
-        fqdn: homeassistant
-  republic-laptop:
-    kind: workstation
-    os: linux
-    role: primary-dev
-    mesh:
-      netbird:
-        fqdn: republic-laptop.netbird.selfhosted
-    ssh:
-      user: dtoro
-  mac-mini:
-    kind: workstation
-    os: macos
-    role: dev
-    lan_ip: 192.168.178.182
-    mesh:
-      netbird:
-        fqdn: mac-mini-234-17.netbird.selfhosted
-    ssh:
-      user: dtoro
-    notes:
-    - Only macOS in the fleet. Bootstrap uses launchd.
-    age_pubkey: age169104ee1a9e1577d493820830560197f0adf56bf8f1c369d57c152c03f9437ae
-  strong:
-    kind: proxmox-host
-    os: linux
-    role: hypervisor
-    lan_ip: 192.168.178.181
-    ssh:
-      user: root
-    notes:
-    - Reformatted from Linux workstation ("ludo-mini" in this wiki, still
-      the machine's nickname) to Proxmox VE 9.2.3 on 2026-07-01. Renamed
-      the inventory/wiki identity from ludo-mini to strong on the same day
-      so it matches the OS/cluster hostname everywhere (bootstrap looks up
-      hosts/$(hostname).yaml, so a mismatch would break enrollment).
-    - Joined hubris's "Homelab" cluster same day. 2-node, no QDevice
-      tiebreaker yet — see hosts/hubris.md quorum note.
-    - Netbird not yet installed (fresh OS wiped prior enrollment); reachable
-      today only via the household LAN / existing Fritz static route to
-      192.168.8.0/24. Re-enroll in mesh as a follow-up if off-LAN access
-      to this host itself (not just its future guests) is needed.
-    - First step of the planned library-SSD migration — see
-      .nomos/plans/2026-06-03_110000-library-ssd-migration-to-ludo-mini.md
-      (filename kept as-is, it's a historical planning doc). Only Phase 1
-      (Proxmox install + cluster join) is done; no physical
-      drive move, service migration, or GPU passthrough has happened yet.
-    age_pubkey: age1rtwvdct6avjkr3cyxv3vue3vqx4d524fjfr3vk7xrnvyrylnry5sm54sn4
-  netbird-vps:
-    kind: external
-    os: linux
-    role: netbird-mgmt
-    mesh:
-      netbird:
-        ip: 100.122.165.149
-        fqdn: netbird-ionos.netbird.selfhosted
-    ssh:
-      user: root
-    notes:
-    - Public IONOS VPS — hosts the vanilla netbird mgmt+signal+relay+dashboard
-      stack + host coturn (see infrastructure/vps-hardening.md +
-      infrastructure/mesh.md changelog 2026-05-21).
-    - NOT a homelab client. No /etc/age/key.txt, no /opt/homelab-context
-      clone. Managed via ssh from hubris; sshd is locked to hubris's pubkey.
-    - Public IPv4 82.165.190.79. Auto-patching via unattended-upgrades.
-    - Configs rendered by `homelab render-vps-configs` from
-      vps/turnserver.conf.tmpl + vps/management.json.tmpl, with secrets
-      decrypted from secrets/turn-shared-secret.yaml +
-      secrets/netbird-authentik-oidc.yaml on hubris.
-  rclone:
-    kind: lxc
-    os: linux
-    role: backup
-    mesh:
-      netbird:
-        fqdn: rclone.netbird.selfhosted
-    age_pubkey: age1pwtdws2thdh7vzp2dzttl3zxgcs2tgpcsjsqgw3q04nyml4kvuqq467u4x
-
-# Destroyed nodes (lifecycle state: destroyed — see oikos/ontology.yaml).
-# Kept so agents can answer "what happened to X?" from structured data and
-# so drift detectors can flag anything still referencing them.
-# Full narrative table: containers/index.md "Recently destroyed".
-archaeology:
-  claudio-bot:
-    kind: lxc
-    pve_id: 123
-    destroyed: 2026-06-04
-    reason: replaced by Nomos Agent on mac-mini; monitoring moved to homelab-health-watchdog cron
-  plato:
-    kind: lxc
-    pve_id: 126
-    destroyed: 2026-06-28
-    reason: notes workspace decommissioned; data retained at /mnt/library/documents/plato
-  mule-photos-new:
-    kind: lxc
-    pve_id: 127
-    destroyed: 2026-05-22
-    reason: PhotoPrism test stack promoted to LXC 120 (Mulimage 2.0 merge)
-  heaper:
-    kind: lxc
-    pve_id: 116
-    destroyed: 2026-05-14
-    reason: decommissioned; data retained at /mnt/library/heaper
-  syncthing:
-    kind: lxc
-    pve_id: 109
-    destroyed: 2026-05-14
-    reason: decommissioned; library subtree was empty
-  seafile:
-    kind: lxc
-    pve_id: 125
-    destroyed: 2026-05-13
-    reason: Seafile Pro evaluation rejected; files.hubris.network removed from caddy + dns
-  arr-yunohost:
-    kind: lxc
-    pve_id: 100
-    destroyed: 2026-04-28
-    reason: migrated to docker stack on arriman (LXC 122)
-  flaresolverr:
-    kind: lxc
-    pve_id: 106
-    destroyed: 2026-04-28
-    reason: folded into the arriman docker compose
-  marimo:
-    kind: lxc
-    pve_id: 107
-    destroyed: 2026-04-28
-    reason: decommissioned
-  photoprism:
-    kind: lxc
-    pve_id: 110
-    destroyed: 2026-04-28
-    reason: replaced by mule-images (LXC 120)
-  karakeep:
-    kind: lxc
-    pve_id: 111
-    destroyed: 2026-04-28
-    reason: decommissioned
-  immich:
-    kind: lxc
-    pve_id: 112
-    destroyed: 2026-04-28
-    reason: replaced by mule-images (LXC 120)
-  reticulum:
-    kind: lxc
-    pve_id: 115
-    destroyed: 2026-04-28
-    reason: decommissioned

plans/2026-07-17-codebase-review-and-cleanup.md

@@ -322,14 +322,17 @@ Remaining brittle numbers (left as-is, intrinsic to evidence trail):
   evidence trail. Recommend adding a "Last verified: YYYY-MM-DD" header to that
   file and a scheduled re-verification (see §F).
 
-### D.3 Substrate docs describing deleted Python architecture — NOT fixed
+### D.3 Substrate docs describing deleted Python architecture — fixed in R5
 
-`.agents/domains/knowledge/schema.md` and `.agents/shared/llm-wiki.md`
+`.agents/domains/knowledge/schema.md` and `.agents/shared/llm-wiki.md` previously described
-describe `bin/homelab`, `oikos/cards/`, `oikos/ledger.py`, root
+`bin/homelab`, `oikos/cards/`, `oikos/ledger.py`, root `inventory.yaml`, `knowledge/sources/`,
-`inventory.yaml`, `knowledge/sources/`, `get_page`/`search_docs` MCP tools —
+`get_page`/`search_docs` MCP tools — none of which exist. **Rewritten** for the DB-native model
-none of which exist. They contradict AGENTS.md §"Source of truth" and ADR
+(ADR 0003): DB is the single source of truth for both structured data and narrative knowledge;
-0003. **These need a full rewrite** (deferred — substantial; tracked as
+`seeds/*.yaml` are the bootstrap+DR manifests; `archive/knowledge/` is the frozen legacy wiki;
-recommendation R5).
+MCP `search_knowledge`/`get_entity_knowledge` replace `get_page`/`search_docs`. Substrate refs in
+`.agents/shared/{writing-style,page-templates}.md` and
+`.agents/domains/operations/schema.md` swept clean. Root `inventory.yaml` marked deprecated
+(stub points to `seeds/inventory.yaml` + DB; full on-client path reconciliation deferred to R13).
 
 ### D.4 ADR format
 
@@ -362,13 +365,14 @@ itself use `/opt/homelab/`. **Pick one and use consistently** (recommend
 `/opt/homelab/` per `CLIENTS.md:70-71`). Deferred — touches many lines and
 the actual deployed path needs confirming against an enrolled client.
 
-### D.8 Legacy root `inventory.yaml`
+### D.8 Legacy root `inventory.yaml` — deprecated in R5
 
-20387-byte Python-era file still committed; superseded by
+20387-byte Python-era file superseded by `seeds/inventory.yaml` on 2026-07-07. **Replaced with a
-`seeds/inventory.yaml` on 2026-07-07. Multiple `.agents/` docs still treat bare
+deprecation stub** pointing to `seeds/inventory.yaml` and the DB (ADR 0003). Kept as a stub rather
-`inventory.yaml` as the kernel source of truth. **Delete or mark explicitly
+than deleted because AGENTS.md §1/§2 still point clients at `/opt/homelab-context/inventory.yaml`
-deprecated** (deferred — touches `.agents/shared/*` and `.agents/domains/*`
+(the on-client clone path); full path reconciliation is R13. `.agents/shared/*` and
-which need the substrate rewrite in R5 anyway).
+`.agents/domains/*` references to bare `inventory.yaml` swept to `seeds/inventory.yaml` or
+qualified as `archive/knowledge/` history.
 
 ## E. Build & tooling
 
@@ -401,7 +405,7 @@ behavior; tracked as R6.
 | R2 | Delete dead web: 21-file tool-renderer registry, 5 dead components, 2 dead store exports, 2 dead npm deps | S | Low | ✅ done (c3973e7+1) |
 | R3 | Decide sqlc vs raw SQL: delete 17 dead queries OR migrate inline SQL to use them | M | Medium | ✅ done (hybrid: 8 deleted, 9 migrated) |
 | R4 | Split `phase3.go` (2627 lines) into per-resource files; refactor `newServer` (708 lines) to a tool registry | M | Medium |
-| R5 | Rewrite `.agents/domains/knowledge/schema.md` + `.agents/shared/llm-wiki.md` for the DB-native model; delete/deprecate root `inventory.yaml` | M | Low |
+| R5 | Rewrite `.agents/domains/knowledge/schema.md` + `.agents/shared/llm-wiki.md` for the DB-native model; delete/deprecate root `inventory.yaml` | M | Low | ✅ done |
 | R6 | Inject desktop `version` from `VERSION` via ldflags; fix `Makefile` `BINARY` colliding with `oikos/` dir | S | Low |
 | R7 | Add tests for `learning` (80% gate), `actuator`, `scheduler`, `domain`, `notifier`, `knowledge` | L | Low |
 | R8 | Add `eslint`+`prettier`+`vitest` to `web/`; wire `svelte-check`+`tsc` into CI; add `web/` CI job | M | Low |