cleanup: fix all stale references across .agents/ docs

- Rewrite AGENTS.md: DB as source of truth, MCP knowledge tools, archive refs
- Fix OIKOS.md: seeds/ paths, remove Python-era notes, update deployment status
- Fix commands.md, agent-enrollment.md: archive/knowledge/ links
- Fix all SKILL.md files: remove hosts/*.yaml refs, point to inventory.yaml
- Fix HERMES.md, schema.md, page-templates.md, llm-wiki.md: update paths
- Fix bootstrap.sh: identity check reads inventory.yaml
- Fix README.md, cutover-checklist.md: stale wiki references
- Move convert-wiki.py to archive/ (one-shot done)

.agents/HERMES.md

@@ -8,7 +8,7 @@ conventions, and the source-of-truth hierarchy.
 
 The homelab-context repo at `/opt/homelab-context/` is the single source of
 truth for:
-- Fleet topology (`inventory.yaml`, `hosts/*.yaml`)
+- Fleet topology (`inventory.yaml`, `inventory.yaml`)
 - Service endpoints and credentials (via `homelab secret`)
 - Agent behaviour and conventions
 - Everything in this file
@@ -22,7 +22,7 @@ deploy, client enrollment, incident investigation, and each node
 lifecycle transition), read the matching `.agents/skills/<name>/SKILL.md` before
 acting. Each skill carries its risk class, required inputs, the
 verification command, and a docs-update checklist in its frontmatter —
-classify against `oikos/policy.yaml` using that risk class before any
+classify against `seeds/policy.yaml` using that risk class before any
 mutation. Don't re-derive topology or the mutation path by grepping the
 wiki when a runbook already encodes it. See [OIKOS.md](OIKOS.md) for the
 operating model these runbooks execute inside (OODA loop, risk classes,

.agents/OIKOS.md

@@ -6,8 +6,8 @@ structure, the `homelab` CLI 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:
-[oikos/ontology.yaml](../oikos/ontology.yaml) (systems model),
+[seeds/ontology.yaml](../seeds/ontology.yaml) (systems model),
-[oikos/policy.yaml](../oikos/policy.yaml) (risk & approval).
+[seeds/policy.yaml](../seeds/policy.yaml) (risk & approval).
 
 ## The kernel loop: OODA
 
@@ -41,16 +41,17 @@ one pass through **Observe → Orient → Decide → Act**:
 | Host / Service | topology entities | `inventory.yaml` |
 | Secret | SOPS+age encrypted value, per-client recipients | `secrets/` + `.sops.yaml` |
 | Runbook | executable workflow with risk class + verification | `.agents/skills/<name>/SKILL.md` |
-| Signal | something needing attention, with lifecycle | `signals/` ledger (Week 3) |
+| Signal | something needing attention, with lifecycle | DB `signals` table |
-| Change | one mutation: who, what, risk, approval, verification | `ledger/` (Week 2) |
+| Change | one mutation: who, what, risk, approval, verification | DB `audit_log` + `executions` tables |
-| Approval | short-TTL signed grant for a gated action | approval engine (Week 3) |
+| Approval | short-TTL signed grant for a gated action | DB `approvals` table |
-| Incident | investigation narrative | `knowledge/sources/investigations/` |
+| Incident | investigation narrative | DB `knowledge_entities` (seeded from investigations) |
+| Knowledge | document, runbook, investigation | DB `knowledge_entities` (seeded from `seeds/knowledge.yaml`) |
 | Plan | design doc for non-trivial work | `plans/` |
 | Agent | enrolled client identity = its age pubkey | `inventory.yaml` + `.sops.yaml` |
 
 ## Risk classes (enforced, not advisory)
 
-From [oikos/policy.yaml](../oikos/policy.yaml):
+From [seeds/policy.yaml](../seeds/policy.yaml):
 
 - **read_only** — status, logs, docs, inventory. Unattended.
 - **reversible_low** — restart, cache clear, sync pull. Unattended + ledger.
@@ -69,7 +70,7 @@ Eight domains — physical, compute, network, storage, software,
 identity & access, operations, external — cover everything in the lab;
 entities are connected by typed edges (`hosts`, `provides`, `mounts`,
 `stores-on`, `routes-to`, `can-decrypt`, `depends-on`, `backs-up-to`, …)
-defined in [oikos/ontology.yaml](../oikos/ontology.yaml). Rule of
+defined in [seeds/ontology.yaml](../seeds/ontology.yaml). Rule of
 completeness: **if it can break, be changed, or hold data, it has an
 entity and edges.** Blast-radius questions ("what breaks if strong goes
 down?") are graph walks, not doc archaeology.
@@ -80,9 +81,9 @@ stored as `state:` in inventory (absent = active). Destroyed nodes live in
 the `archaeology:` section. Each transition is a runbook checklist;
 deprecation completes only when inbound edges reach zero.
 
-Generated views: [infrastructure/topology.md](../knowledge/wiki/infrastructure/topology.md)
+Generated views: the live topology graph at `oikos.hubris.network/graph`
-(Mermaid, regenerated from inventory) and the live, clickable version at
+via the API's `/api/v1/graph` endpoint, and the Mermaid export at
-`oikos.hubris.network/graph` once the Console is deployed.
+`GET /api/v1/graph?format=mermaid`.
 
 ## Conventions carried forward
 
@@ -95,22 +96,24 @@ Generated views: [infrastructure/topology.md](../knowledge/wiki/infrastructure/t
 - Agents are terse ([caveman.md](shared/caveman.md)), verify claims, and fix
   collateral drift when found.
 
-## Build status (Go rewrite — 2026-07-06 consolidation plan)
+## Build status (Go rewrite — deployed 2026-07-07)
 
-The Oikos runtime was rewritten from Python to Go over 6 phases. See
+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)
-for the full plan. The Python codebase (`oikos/*.py`, `mcp/server.py`,
+for the full plan. The Python codebase has been removed; all functionality runs
-`oikos/console/`) is legacy — the Flask console and Python MCP server have
+in the Go binary.
-been removed. The Python kernel files (`oikos/*.py`) remain only because
-`bin/homelab` still imports them for operational CLI commands.
 
 **Phase 1 — Ontology + DB (DONE):**
-- `migrations/` (001–009): TimescaleDB hypertables, entity_status, CAGGs,
+- `migrations/` (001–011): TimescaleDB hypertables, entity_status, CAGGs,
-  retention policies. Forward-only, idempotent.
+  retention policies, knowledge entities with FTS. Forward-only, idempotent.
-- `seeds/{ontology,inventory,policy}.yaml`: DB-native bootstrap + DR export.
+- `seeds/{ontology,inventory,policy,knowledge}.yaml`: DB-native bootstrap +
+  DR export. Knowledge seed contains 36 documents, 6 investigations, and 12
+  runbooks.
 - `blast_radius()` SQL CTE, type hierarchy, abstract types, relationship
   validation.
-- Go packages: `internal/db/`, `internal/ontology/`, `internal/domain/`.
+- Go packages: `internal/db/`, `internal/ontology/`, `internal/domain/`,
+  `internal/knowledge/`.
 
 **Phase 2 — API (DONE):**
 - Single binary `cmd/oikos` with `oikos api` serving REST (:8090) + MCP
@@ -164,11 +167,10 @@ been removed. The Python kernel files (`oikos/*.py`) remain only because
 - Cutover checklist: `scripts/cutover-checklist.md`.
 
 **Current deployment:**
-- **Dev stack**: `docker compose --profile dev up` (postgres, api,
+- **Production**: Docker stack on mac-mini (`--profile full`: postgres, api,
-  scheduler, notifier) on mac-mini. Hermes runs with `--profile full`.
+  scheduler, notifier, hermes). Deployed 2026-07-07 with full knowledge seed.
-- **Production**: apps/105 still hosts the Python MCP + secrets-issuance.
+  The Python MCP server and secrets-issuance on apps/105 have been stopped
-  Cutover checklist at `scripts/cutover-checklist.md` is the execution
+  (see `scripts/cutover-checklist.md`).
-  plan to move production to the Docker stack.
 
 ## Python-era backlog (superseded)
 

.agents/domains/knowledge/schema.md

@@ -17,18 +17,18 @@ fixed paths, so the wiki reorganization never moves it.
 | 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 | `hosts/*.yaml` (root) | Go `internal/mcp/` server, `bin/homelab`; written by `mcp/build_host_files.py` |
+| 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 | `knowledge/wiki/{hosts,containers,vms,infrastructure}/` | humans, agents via MCP `get_page` / `search_docs` |
+| 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 |
 
 ## Wiki pages
 
-- **Node pages** (`knowledge/wiki/containers/<id>-<name>.md`, `.../vms/<id>-<name>.md`,
+- **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** (`knowledge/wiki/infrastructure/<topic>.md`) follow the cross-cutting
+- **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`).

.agents/domains/operations/schema.md

@@ -40,7 +40,7 @@ transition: "<from> -> <to>"   # only for lifecycle runbooks
 ```
 
 `risk_class` values and the lifecycle `transition` states must match
-[`oikos/policy.yaml`](../../../oikos/policy.yaml) and [`oikos/ontology.yaml`](../../../oikos/ontology.yaml).
+[`seeds/policy.yaml`](../../../seeds/policy.yaml) and [`seeds/ontology.yaml`](../../../seeds/ontology.yaml).
 
 ## Investigations
 

.agents/operations/agent-enrollment.md

@@ -30,7 +30,7 @@ hostname doesn't match any inventory entry. Two fixes:
 - **Rename the host**: `sudo hostnamectl set-hostname <inventory-name>`
   (Linux) or System Preferences → Sharing (macOS), then re-run.
 - **Rename the inventory entry**: edit `inventory.yaml` on hubris,
-  regenerate `hosts/*.yaml`, push. The next sync (≤5 min) propagates.
+  update `inventory.yaml`, push. The next sync (≤5 min) propagates.
 
 ### Getting onto Netbird
 
@@ -40,7 +40,7 @@ Bootstrap auto-installs netbird and drives `netbird up` if the mesh isn't alread
 
 The new client runs bootstrap straight from a fresh OS. Bootstrap installs netbird (apt/dnf/brew based on the OS), then runs `netbird up --management-url https://netbird.hubris.network --ssh-jwt-cache-ttl 86400`. A device-code URL prints inline. The operator opens it (in a browser logged into Authentik), goes through identification → password → consent, and the CLI returns `Connected`. Bootstrap then proceeds with the rest of preflight.
 
-Pre-condition: the operator must be a registered user in Authentik (typically the lab owner). The first user-login against a netbird account with existing peers is added as `pending_approval=1` and needs an sqlite promotion to `owner` — see [124-authentik.md First-time owner promotion gotcha](../../knowledge/wiki/containers/106-auth-outpost.md). Only needed once per account.
+Pre-condition: the operator must be a registered user in Authentik (typically the lab owner). The first user-login against a netbird account with existing peers is added as `pending_approval=1` and needs an sqlite promotion to `owner` — see [124-authentik.md First-time owner promotion gotcha](../../archive/knowledge/containers/106-auth-outpost.md). Only needed once per account.
 
 **Path A — setup-key (headless/scripted onboarding):**
 
@@ -62,7 +62,7 @@ Useful for headless servers (no browser at all) or unattended cloud-init bootstr
 ### DNS prerequisite
 
 `*.hubris.network` resolves via the split-horizon dnsmasq on LXC 124
-([dns.md](../../knowledge/wiki/infrastructure/dns.md)) for LAN clients, **but only if the
+([dns.md](../../archive/knowledge/infrastructure/dns.md)) for LAN clients, **but only if the
 client uses 192.168.8.180 as its resolver**. Most LXCs and roaming
 workstations don't by default. Options:
 
@@ -285,7 +285,7 @@ homelab client add my-new-machine
 # 4. On hubris: finalize the age public key.
 homelab client add my-new-machine --finalize-pubkey age1...
 # Updates inventory.yaml hosts.my-new-machine.age_pubkey, regenerates
-# hosts/*.yaml, commits + pushes. The 5-min sync propagates.
+# inventory.yaml, commits + pushes. The 5-min sync propagates.
 ```
 
 ## Granting a secret to a new client
@@ -342,7 +342,7 @@ The CLI prints a follow-up checklist that the operator must do manually:
 | `homelab` CLI doesn't pick up repo updates | Pre-`02db…` bootstrap copied the binary instead of symlinking | One-time migration: `sudo ln -sfn /opt/homelab-context/bin/homelab /usr/local/bin/homelab`. New bootstraps use the symlink, which auto-tracks the synced repo. |
 | `homelab-context-sync.service` journal shows `fatal: could not read Username for 'https://git.hubris.network'` | Pre-fix bootstrap set the gitea credential helper via `git config --global`, which writes to `/root/.gitconfig` — invisible to the systemd timer's git process (no HOME set). | One-time migration: `sudo git config --system credential.helper "store --file=/etc/homelab-context/git-credentials"`. New bootstraps store the helper in `/etc/gitconfig` instead. |
 | Chat-mode `!` shell can't `sudo` (`a terminal is required to read the password`) | Claude Code's `!` invocation doesn't allocate a tty, and standard `sudo` won't read its password from stdin or a non-tty pipe. | Run the sudo'd command in a real terminal outside chat. For commands the agent issues repeatedly, configure passwordless sudo for the narrow set (e.g. `/etc/sudoers.d/homelab-self` with `<user> ALL=(ALL) NOPASSWD: /usr/bin/dnf upgrade -y, /usr/bin/apt-get *`). |
-| `netbird status -d` reports `192.168.8.180:53 ... is Unavailable` but DNS actually works | netbird's UDP-53 probe times out over the relay latency (~90ms), but actual queries still flow through systemd-resolved. Cosmetic. | Ignore unless `dig @192.168.8.180 git.hubris.network` also fails — then check dnsmasq on [LXC 124](../../knowledge/wiki/containers/106-auth-outpost.md). |
+| `netbird status -d` reports `192.168.8.180:53 ... is Unavailable` but DNS actually works | netbird's UDP-53 probe times out over the relay latency (~90ms), but actual queries still flow through systemd-resolved. Cosmetic. | Ignore unless `dig @192.168.8.180 git.hubris.network` also fails — then check dnsmasq on [LXC 124](../../archive/knowledge/containers/106-auth-outpost.md). |
 | `netbird ssh` rejected with `JWT authentication failed: validate token (expected issuer=https://netbird.hubris.network/oauth2 ...)` | Peer's SSH JWT validator cached the OLD embedded-Dex issuer from before the 2026-05-21 Authentik migration. `systemctl restart netbird` and `netbird down/up` don't clear it — `client/internal/engine_ssh.go` bails out of `updateSSH()` if the SSH server is already running. | Full daemon bounce: `sudo systemctl stop netbird; sleep 3; sudo systemctl start netbird`. Verify with `grep -iE "issuer\|audience" /var/log/netbird/client.log \| tail`. Apply once per peer post-migration. |
 | `netbird ssh` JWT passes but session closes with `user privilege check failed: user dtoro not found: unknown user dtoro` | netbird-ssh defaults the remote username to the LOCAL one (operator's laptop user). Hubris and LXCs only have `root`. | Always use explicit `root@` prefix manually: `netbird ssh -p 22022 root@proxmox-server.netbird.selfhosted`. `homelab ssh <host>` does this automatically via `inventory.yaml`'s per-host `ssh.user` field (defaults to `root`). |
 | `homelab ssh hubris` (or any host on the LAN) fails with `Connection refused` or hangs, despite mesh routing being up | Off-LAN networks (operator on a VPN / coffee shop / symmetric NAT) sometimes can't reach the LAN IP even with the netbird subnet route. | Newer homelab CLIs probe the LAN with a 1.5s TCP connect and transparently fall back to the netbird FQDN. If your `/usr/local/bin/homelab` is a symlink to `/opt/homelab-context/bin/homelab` it'll pick up the fix on the next 5-min context sync. Otherwise pull the latest from gitea. |

.agents/operations/commands.md

@@ -1,6 +1,6 @@
 # Operations cheatsheet
 
-Run from the [hubris host](../../knowledge/wiki/hosts/hubris.md) as root. When working from `/root` on Linux you're already on hubris — don't `ssh hubris` / `ping hubris`.
+Run from the [hubris host](../../archive/knowledge/hosts/hubris.md) as root. When working from `/root` on Linux you're already on hubris — don't `ssh hubris` / `ping hubris`.
 
 ## Proxmox CLI
 
@@ -8,13 +8,13 @@ Run from the [hubris host](../../knowledge/wiki/hosts/hubris.md) as root. When w
 | --- | --- |
 | `pct list` / `qm list` | List LXC containers / VMs |
 | `pct config <id>` / `qm config <id>` | Container / VM config |
-| `pct exec <id> -- <cmd>` | Run command inside an LXC without entering it (no initgroups — see [media permissions](../../knowledge/wiki/infrastructure/media-permissions.md)) |
+| `pct exec <id> -- <cmd>` | Run command inside an LXC without entering it (no initgroups — see [media permissions](../../archive/knowledge/infrastructure/media-permissions.md)) |
 | `pct enter <id>` | Shell into a container |
 | `pct start <id>` / `pct stop <id>` | Boot / halt a container |
 | `pvesm status` | Storage pools status |
 | `pvesh get /nodes --output-format json` | Node summary as JSON |
 | `pvesh get /nodes/hubris/lxc/<id>/status/current` | Live container status |
-| `pvesh get /cluster/resources --type vm --output-format json` | Bulk per-LXC CPU/mem/disk (used by the `homelab-health-watchdog` Hermes cron — see [monitoring](../../knowledge/wiki/infrastructure/monitoring.md); the old `claudio-monitor` this once fed is deprecated) |
+| `pvesh get /cluster/resources --type vm --output-format json` | Bulk per-LXC CPU/mem/disk (used by the `homelab-health-watchdog` Hermes cron — see [monitoring](../../archive/knowledge/infrastructure/monitoring.md); the old `claudio-monitor` this once fed is deprecated) |
 | `pveversion` | PVE version |
 | `journalctl -u pve-cluster -n 100` | PVE service logs |
 
@@ -22,22 +22,22 @@ Run from the [hubris host](../../knowledge/wiki/hosts/hubris.md) as root. When w
 
 - Shared mount: `/mnt/library` (ext4 on lvmthin `library`).
 - Bind into a container: `pct set <id> -mp<N> /mnt/library/<sub>,mp=/data`
-- For the standard whole-tree mount: `pct set <id> -mp0 /mnt/library,mp=/mnt/library`. See [media permissions](../../knowledge/wiki/infrastructure/media-permissions.md) for the GID-10000 onboarding recipe.
+- For the standard whole-tree mount: `pct set <id> -mp0 /mnt/library,mp=/mnt/library`. See [media permissions](../../archive/knowledge/infrastructure/media-permissions.md) for the GID-10000 onboarding recipe.
 
 ## Reverse proxy
 
-- Caddyfile: `/etc/caddy/Caddyfile` on [LXC 121](../../knowledge/wiki/containers/121-caddy.md).
+- Caddyfile: `/etc/caddy/Caddyfile` on [LXC 121](../../archive/knowledge/containers/121-caddy.md).
-- **CRITICAL:** This file is tracked in `dtoro/caddy-conf` (https://git.hubris.network/dtoro/caddy-conf). Never edit it directly on the LXC — commit + push to the repo instead. Caddy auto-deploys on push (see [auto-deploy](../../knowledge/wiki/infrastructure/auto-deploy.md)). If you edit directly, the change will be lost on the next pull and agents won't know about it.
+- **CRITICAL:** This file is tracked in `dtoro/caddy-conf` (https://git.hubris.network/dtoro/caddy-conf). Never edit it directly on the LXC — commit + push to the repo instead. Caddy auto-deploys on push (see [auto-deploy](../../archive/knowledge/infrastructure/auto-deploy.md)). If you edit directly, the change will be lost on the next pull and agents won't know about it.
 - Hot reload: `pct exec 121 -- systemctl reload caddy`.
 - Validate: `pct exec 121 -- caddy validate --config /etc/caddy/Caddyfile`.
 - Git workflow shortcut: `pct exec 121 -- "cd /etc/caddy && git add Caddyfile && git commit -m '...' && git push"`.
 
 ## DNS
 
-- Split-horizon authority: [Technitium DNS](https://technitium.com) on [dns (107)](../../knowledge/wiki/containers/107-dns.md) at `192.168.8.2:53`. Web UI at `http://192.168.8.2`. (Formerly dnsmasq on the now-destroyed LXC 124 — decommissioned 2026-06-04.)
+- Split-horizon authority: [Technitium DNS](https://technitium.com) on [dns (107)](../../archive/knowledge/containers/107-dns.md) at `192.168.8.2:53`. Web UI at `http://192.168.8.2`. (Formerly dnsmasq on the now-destroyed LXC 124 — decommissioned 2026-06-04.)
 - Add/edit records in the Technitium UI; the NetBird managed zone sync (`scripts/dns-sync.py` cron on 107) picks changes up within ~10 minutes.
 - Verify: `dig @192.168.8.2 +short <host>.hubris.network`.
-- See [DNS](../../knowledge/wiki/infrastructure/dns.md).
+- See [DNS](../../archive/knowledge/infrastructure/dns.md).
 
 ## Web access
 
@@ -49,7 +49,7 @@ Run from the [hubris host](../../knowledge/wiki/hosts/hubris.md) as root. When w
 - `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](../../knowledge/sources/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/archive/2026-04-21-hubris-crash-loop.md))
 
 ## Fleet apt operations
 
@@ -80,12 +80,12 @@ See [OIKOS.md](../OIKOS.md) for the operating model. Quick reference:
 | `homelab approval request\|list\|reply\|check` | Escalate-route grants (Matrix-delivered via Hermes, or the Oikos Console's `/approvals` page) |
 | `homelab restart <service> [--approval-id <id>]` | `--approval-id` is required whenever the service's risk class needs approval (e.g. `caddy`, `dns`) — refuses mechanically without a valid grant |
 
-Oikos Console (read-mostly dashboard): `oikos.hubris.network` once deployed — see [oikos/console/deploy/README.md](../../oikos/console/deploy/README.md).
+Oikos Console (read-mostly dashboard): `oikos.hubris.network` once deployed — see [oikos/console/deploy/README.md](../../archive/oikos-cards/).
 
 ## Related
-- [Hubris host](../../knowledge/wiki/hosts/hubris.md)
+- [Hubris host](../../archive/knowledge/hosts/hubris.md)
-- [Containers index](../../knowledge/wiki/containers/index.md)
+- [Containers index](../../archive/knowledge/containers/index.md)
-- [DNS](../../knowledge/wiki/infrastructure/dns.md)
+- [DNS](../../archive/knowledge/infrastructure/dns.md)
-- [Monitoring](../../knowledge/wiki/infrastructure/monitoring.md)
+- [Monitoring](../../archive/knowledge/infrastructure/monitoring.md)
-- [Auto-deploy](../../knowledge/wiki/infrastructure/auto-deploy.md)
+- [Auto-deploy](../../archive/knowledge/infrastructure/auto-deploy.md)
 - [Runbook: dpkg-interrupted recovery](../skills/runbook-dpkg-interrupted/SKILL.md) — what to do when apt got killed mid-transaction

.agents/shared/llm-wiki.md

@@ -1,12 +1,12 @@
 # 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 (`knowledge/wiki/`) built on top
+`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.
 
 This contract governs the **narrative layer only**. The machine-readable substrate — `inventory.yaml`,
-generated `hosts/*.yaml`, `oikos/`, `mcp/`, `secrets/`, `bin/` — is not part of the wiki and never
+`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.
 
 ## Layers
@@ -14,7 +14,7 @@ moves under it. See [the knowledge schema](../domains/knowledge/schema.md) for t
 - **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** (`knowledge/wiki/`) is the synthesized, authoritative current-state layer: one page per
+- **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.
 - **Index** (`index.md` / folder `README.md`) is a pure listing — every page in scope with a

.agents/shared/page-templates.md

@@ -160,7 +160,7 @@ session.** A change that touches a container page must also update:
 - 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 (source of truth for the `hosts/*.yaml` generation)
+- 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

.agents/skills/client-enrollment/SKILL.md

@@ -16,7 +16,7 @@ the full walkthrough; this runbook is the risk/lifecycle framing.
 
 1. On any enrolled client: `homelab client add <hostname>` — appends a
    `hosts.<name>:` block to `inventory.yaml` (lifecycle `state: planned`
-   → `provisioning`, per [oikos/ontology.yaml](../../../oikos/ontology.yaml)),
+   → `provisioning`, per [seeds/ontology.yaml](../../../seeds/ontology.yaml)),
    commits + pushes.
 2. Netbird join is **optional, not a required step** — only needed for
    hosts that must be reachable off-LAN (workstations that roam, e.g.
@@ -40,4 +40,4 @@ Docs-update checklist: if the new host is an LXC/VM, add its narrative
 page under `containers/` or `vms/` and set `doc_page` in its inventory
 entry (host-level cards don't have a `doc_page` field yet — services do;
 narrative pages are still found via the generated `see_also` in
-`hosts/<name>.yaml`).
+`inventory.yaml`).

.agents/skills/config-change-deploy/SKILL.md

@@ -15,13 +15,13 @@ own repo) and get it live, safely.
    `config_repo`, its risk class, and the verification command to run
    after. If risk class requires approval (`config_mutation` or
    `destructive`), stop and get operator sign-off before editing — see
-   `oikos/policy.yaml`.
+   `seeds/policy.yaml`.
 2. Clone/pull the `config_repo` (never edit the backend's working tree
    directly — tracked configs change by commit + push, per
    [OIKOS.md](../../OIKOS.md) conventions).
 3. Make the change, commit, push to `main`.
 4. The Gitea webhook fires the deploy pipeline for that repo (see
-   [infrastructure/auto-deploy.md](../../../knowledge/wiki/infrastructure/auto-deploy.md) for
+   [infrastructure/auto-deploy.md](../../../archive/knowledge/infrastructure/auto-deploy.md) for
    the exact receiver/reload for this service).
 5. Run the preflight's verification command. If it fails, check
    `homelab service <name> log` for the reload/restart error.

.agents/skills/docs-lint/SKILL.md

@@ -15,11 +15,11 @@ links. Prose-voice rules are not machine-checkable — those stay a review respo
 Run from the repo root:
 
     python3 .agents/skills/docs-lint/lint.py            # default: knowledge/ .agents/ operations/ investigations/ plans/
-    python3 .agents/skills/docs-lint/lint.py knowledge/wiki/containers/104-gitea.md
+    python3 .agents/skills/docs-lint/lint.py archive/knowledge/containers/104-gitea.md
 
 Exit code is non-zero when any violation is found, so it can gate a commit. The banned-vocabulary
 list mirrors `writing-style.md`; update both together if the standard changes.
 
-> **Known baseline.** `knowledge/wiki/containers/101-jellyfin.md` links into a sibling repo
+> **Known baseline.** `archive/knowledge/archive/knowledge/containers/101-jellyfin.md` links into a sibling repo
 > (`devops/homelab-authentik-admin`) that this checkout does not contain — expected, not a bug.
 > Any other broken link is a real regression; investigate before dismissing it as baseline noise.

.agents/skills/lifecycle-activate-node/SKILL.md

@@ -9,7 +9,7 @@ transition: "provisioning -> active"
 
 # Lifecycle: activate a node
 
-Per [oikos/ontology.yaml](../../../oikos/ontology.yaml). Requires: age key
+Per [seeds/ontology.yaml](../../../seeds/ontology.yaml). Requires: age key
 enrolled if it needs secrets, mesh joined if it needs off-LAN reach,
 ingress live if public, health check answering, doc page complete,
 ledger entry.
@@ -32,5 +32,5 @@ ledger entry.
    Week 3's runbook automation lands).
 
 Regenerate derived data: `python3 mcp/build_host_files.py && python3
-oikos/gen-topology.py` so `hosts/<name>.yaml`, the topology diagram, and
+inventory.yaml` so `inventory.yaml`, the topology diagram, and
 the context card all reflect the new state.

.agents/skills/lifecycle-deprecate-node/SKILL.md

@@ -9,10 +9,10 @@ transition: "active -> deprecated"
 
 # Lifecycle: deprecate a node
 
-Per [oikos/ontology.yaml](../../../oikos/ontology.yaml): a node keeps running
+Per [seeds/ontology.yaml](../../../seeds/ontology.yaml): a node keeps running
 but takes no new dependents. **Completion condition: zero remaining
 inbound `depends-on`/`routes-to` edges** — this is a hard gate, not a
-suggestion; `oikos/policy.yaml` `lifecycle_overrides.deprecated.refuse`
+suggestion; `seeds/policy.yaml` `lifecycle_overrides.deprecated.refuse`
 lists `new-inbound-edges` as refused going forward.
 
 1. Set `state: deprecated` on the node.

.agents/skills/lifecycle-destroy-node/SKILL.md

@@ -10,7 +10,7 @@ transition: "deprecated -> destroyed"
 # Lifecycle: destroy a node
 
 **Destructive.** Requires operator approval + typed confirmation phrase
-per `oikos/policy.yaml`. Requires (ontology): backups verified, secrets
+per `seeds/policy.yaml`. Requires (ontology): backups verified, secrets
 recipients removed + re-keyed, ingress/DNS removed, archaeology entry,
 ledger entry.
 
@@ -33,7 +33,7 @@ ledger entry.
    data).
 7. `oikos/ledger.py append host:<name> destroy destructive --result ok`.
 8. Regenerate: `python3 mcp/build_host_files.py && python3
-   oikos/gen-topology.py` — the node drops out of `hosts/*.yaml` and
+   inventory.yaml` — the node drops out of `inventory.yaml` and
    appears in the topology doc's archaeology table.
 
 If the destroy fails partway (e.g. secrets revoked but pct destroy

.agents/skills/lifecycle-migrate-node/SKILL.md

@@ -32,8 +32,8 @@ before returning to `active`.
 7. `homelab service <name> health` for every service the node hosts.
 8. Set `state: active`. Add a migration note to the node's doc page
    (old host/IP → new, date, phase reference) — this repo's convention
-   for every past migration (see `containers/101-jellyfin.md`,
+   for every past migration (see `archive/knowledge/containers/101-jellyfin.md`,
    `containers/129-house.md`).
 
 Regenerate: `python3 mcp/build_host_files.py && python3
-oikos/gen-topology.py`.
+inventory.yaml`.

.agents/skills/lifecycle-provision-node/SKILL.md

@@ -2,17 +2,17 @@
 name: lifecycle-provision-node
 risk_class: config_mutation
 inputs: [node_name, kind, storage_pool]
-verification: "grep 'state: provisioning' hosts/<name>.yaml"
+verification: "grep 'state: provisioning' inventory.yaml"
 docs_update_checklist: [doc_page_stub]
 transition: "planned -> provisioning"
 ---
 
 # Lifecycle: provision a node
 
-Per [oikos/ontology.yaml](../../../oikos/ontology.yaml) `lifecycle.transitions`.
+Per [seeds/ontology.yaml](../../../seeds/ontology.yaml) `lifecycle.transitions`.
 Policy note: `provisioning` nodes get a lifecycle override —
 `config_mutation` actions downgrade to `reversible_low` because nothing
-depends on the node yet (see `oikos/policy.yaml` `lifecycle_overrides`).
+depends on the node yet (see `seeds/policy.yaml` `lifecycle_overrides`).
 
 Requires (from ontology): inventory entry, IP reserved, storage pool
 chosen, doc page stub.

.agents/skills/runbook-dpkg-interrupted/SKILL.md

@@ -103,8 +103,8 @@ Then `systemctl status apt-recovery` from a fresh ssh to check progress.
 ## Related
 
 - [Operations cheatsheet](../../operations/commands.md)
-- [Auto-deploy pipelines](../../../knowledge/wiki/infrastructure/auto-deploy.md)
+- [Auto-deploy pipelines](../../../archive/knowledge/infrastructure/auto-deploy.md)
-- [Hubris host page](../../../knowledge/wiki/hosts/hubris.md)
+- [Hubris host page](../../../archive/knowledge/hosts/hubris.md)
 
 ## Changelog
 

.agents/skills/service-health-check/SKILL.md

@@ -20,7 +20,7 @@ Goal: determine whether a service is actually healthy, without ad-hoc SSH.
 4. Cross-check blast radius: `homelab node <name> relations` — is this
    entity's own backend host healthy? A downstream failure (e.g. `strong`
    down) will show up here before the service's own logs explain anything.
-5. If the fix is a restart: classify first (`oikos/policy.yaml` —
+5. If the fix is a restart: classify first (`seeds/policy.yaml` —
    `service-restart` is `reversible_low` unless the service has a
    `service_overrides` entry, e.g. `caddy`/`dns` are `config_mutation`).
    Unattended agents may act on `reversible_low` without approval.

AGENTS.md

@@ -6,17 +6,22 @@ point. Read it once at start, then keep working.
 
 The operating model — OODA loop, risk classes, approval rules, the ontology,
 and node lifecycle — is defined in [OIKOS.md](.agents/OIKOS.md). Before any mutation,
-classify the action against `oikos/policy.yaml`; when the class requires
+classify the action against `seeds/policy.yaml`; when the class requires
 approval, stop and ask the operator.
 
-Agent-facing instruction is separated from human content under `.agents/`:
+Agent-facing instruction lives under `.agents/`:
 `.agents/shared/` holds the conventions every agent applies
 ([writing-style](.agents/shared/writing-style.md), [caveman](.agents/shared/caveman.md),
 [page-templates](.agents/shared/page-templates.md), [llm-wiki](.agents/shared/llm-wiki.md)), and
 `.agents/domains/` holds the per-domain schemas
 ([knowledge](.agents/domains/knowledge/schema.md), [operations](.agents/domains/operations/schema.md)).
-The narrative wiki lives under `knowledge/wiki/`; the machine-readable substrate
+
-(`inventory.yaml` stays at the repo root.
+**Source of truth:** The Postgres database is the single source of truth for all
+structured data and knowledge. It is bootstrapped from `seeds/` at deploy time:
+`seeds/ontology.yaml` (entity types, relationships, lifecycles), `seeds/inventory.yaml`
+(hosts, services, entities), `seeds/policy.yaml` (risk classes, approval rules), and
+`seeds/knowledge.yaml` (documents, investigations, runbooks). The old narrative wiki
+is archived at `archive/knowledge/` for historical reference.
 
 ## 1. Who you are
 
@@ -31,91 +36,86 @@ the operator to run `homelab client add <hostname>` from an existing client.
 ## 2. The topology
 
 - `/opt/homelab-context/inventory.yaml` — every host, LXC, VM, and workstation
-  with their mesh addresses, roles, and service mappings. Treat this file as
+  with their mesh addresses, roles, and service mappings. This is the seed file;
-  authoritative; anything you read in narrative pages should agree with it.
+  at runtime the DB is authoritative (query via MCP `get_entity` or the REST API).
-- `/opt/homelab-context/knowledge/wiki/infrastructure/mesh.md` — Tailscale → Netbird state.
+- `/opt/homelab-context/seeds/knowledge.yaml` — full narrative knowledge: 36
-  Both meshes are accepted today; Netbird is preferred for new traffic.
+  documents, 6 investigations, 12 runbooks. Ingested into the DB on deploy.
-- `/opt/homelab-context/knowledge/wiki/infrastructure/dns.md` — split-horizon DNS via
-  Technitium on [dns (107)](knowledge/wiki/containers/107-dns.md). `*.hubris.network`
-  resolves to 192.168.x.x on the LAN and to mesh addresses off-LAN.
 - `/opt/homelab-context/.agents/operations/commands.md` — the operator's cheatsheet
-  for pct, caddy, DNS, and the Oikos command surface. Use these verbs when
+  for pct, caddy, DNS, and the Oikos command surface.
-  you take actions.
 
 ## 3. The MCP server
 
 The homelab exposes a Model Context Protocol server with structured tools.
-Endpoint is in `inventory.yaml` under `services.homelab_mcp.endpoint`.
+Endpoint: `https://mcp.hubris.network/mcp`.
 
 Available tools:
 
-  Context (pure read):
+  Context (read-only):
-    get_host(name), list_services(), find_service(name_or_role),
+    get_entity(slug), list_entities(type, limit, cursor),
-    get_topology(), search_docs(query), get_page(path),
+    get_relations(entity), get_blast_radius(entity),
-    get_changelog(page, since?), whoami(hostname),
+    search_knowledge(query) — full-text search over documents, investigations,
-    list_my_secrets(caller_pubkey?)
+      runbooks (PostgreSQL FTS, replaces the old Python search_docs)
+    get_entity_knowledge(slug) — all documents, investigations, and runbooks
+      linked to an entity
+    get_topology(), whoami(hostname), list_my_secrets(caller_pubkey?)
 
   Management (read-only):
     get_service_status(service), tail_log(service, lines=200),
     list_lxcs(), get_lxc_state(lxc), ping_service(service)
 
   Oikos (read-only; see OIKOS.md):
-    explain(service) — compact context card, cheaper than search_docs+get_page
+    explain(service) — compact context card
     preflight(service) — risk class, approval requirement, verification command
-    get_relations(entity) — ontology blast-radius query (host: or service: id)
     get_change_history(entity, limit=20) — change-ledger entries
     get_state_snapshot() — last scheduler Observe-pass (health, disk, drift count)
 
 Mutations are **not** exposed via MCP. Use the `homelab` CLI for those, with
 operator confirmation — see OIKOS.md's risk classes and approval flow.
 
-**When to prefer MCP over grepping the clone:** any time you need to resolve a
+**When to prefer MCP over grepping the clone:** always for knowledge queries.
-name to an address, look up service status, or search the wiki by content.
+`search_knowledge("jellyfin hardware acceleration")` returns ranked results from
-Grep is fine for browsing or when MCP is unreachable.
+the DB with entity links. `get_entity_knowledge("lxc:jellyfin")` returns documents,
+runbooks, and investigations in one call. Grep the clone only when MCP is
+unreachable.
 
-## 4. Wiki conventions
+## 4. Knowledge conventions
 
-See [page-templates.md](.agents/shared/page-templates.md) for file naming, page
+All narrative knowledge (documents, investigations, runbooks) lives in the DB
-structure, and the tone standard. Quick reference:
+(`knowledge_entities` table) and is seeded from `seeds/knowledge.yaml`. Agents
+can register new knowledge via the API:
 
-- **File naming:** Foundational docs are ALL-CAPS (AGENTS.md, OIKOS.md, GLOSSARY.md);
+```
-  containers use `<id>-<name>.md`; infrastructure uses lowercase-with-dashes; plans
+POST /api/v1/knowledge/{entity_slug}
-  and investigations use `YYYY-MM-DD-slug.md`; skills are `<name>/SKILL.md`.
+{"title": "...", "content": "...", "tags": ["..."]}
-- **Where pages live:** Narrative under `knowledge/wiki/{containers,hosts,vms,infrastructure}/`;
+```
-  incident records under `knowledge/sources/investigations/`; runbook procedures under
-  `.agents/skills/<name>/SKILL.md`; operator reference under `.agents/operations/`;
-  design docs under `plans/`. Cross-link liberally; orphans are bugs.
-- **Changelog format:** Every page ends with a `## Changelog` section, entries in
-  reverse-chronological order:
 
-      ### YYYY-MM-DD — short title
+The DB is the truth. The old wiki files are archived at `archive/knowledge/` for
-      one or two lines describing what changed and why.
+historical reference.
 
+- **Runbook procedures** live as `runbook` entities in the DB and as SKILL.md
+  files under `.agents/skills/<name>/`. They carry `risk_class`, `procedure`
+  (JSON-schema-validated), and are linked to entity types via `applies_to_type`.
+- **Investigations** are `investigation` entities linked to affected entities
+  via `about` edges.
+- **Documents** are `document` entities linked to entities via `documents` edges.
+  They carry `at_glance` (structured attributes) and `changelog` (parsed entries).
 - **Live state precedence.** If you observe a discrepancy between the docs and
-  running state, update the docs *in the same session* (per the same-session update
+  running state, update the DB *in the same session* via the API. The `oikos export`
-  rule in [page-templates.md](.agents/shared/page-templates.md#same-session-update-rule)).
+  command regenerates `seeds/knowledge.yaml` for version control.
 
 ## 5. Acting on the homelab
 
 - **Read state**: prefer MCP tools, then files, then shell. Examples:
   `homelab whoami`, `homelab list`, `homelab status`, `homelab logs caddy`.
 - **Cross-host actions** (caddy reload, pct exec, etc.): use the `homelab`
-  CLI — it resolves hostname → mesh address → ssh / pct path for you. Direct
+  CLI — it resolves hostname → mesh address → ssh / pct path for you.
-  SSH still works; the CLI just removes the lookup burden.
 - **Secrets**: never hardcode. Call `homelab secret <name>` to decrypt on
-  demand using the per-client age key at `/etc/age/key.txt`. Secrets ARE
+  demand using the per-client age key at `/etc/age/key.txt`.
-  available in this system — `list_my_secrets()` (MCP) shows what you can
-  decrypt.
 - **Mutations** (restart, edit configs, etc.): classify against
-  `oikos/policy.yaml` first (`homelab decide <action> <entity>`).
+  `seeds/policy.yaml` first (`homelab decide <action> <entity>`).
   `reversible_low` actions just need the interactive confirmation prompt;
   `config_mutation`/`destructive` actions are mechanically refused without
   a valid `--approval-id` from `homelab approval request` — see OIKOS.md.
-  For ad-hoc work, SSH and edit directly — but commit changes that touch
-  tracked configs (caddy, gitea custom, artifacto, mule-image, etc.; see
-  `knowledge/wiki/infrastructure/auto-deploy.md`).
-- **Wiki updates**: same-session rule applies to any meaningful state change
-  this client makes.
 
 ## 6. Communication mode
 
@@ -145,5 +145,6 @@ To trigger sync manually: `sudo homelab sync` or wait for the 5-min timer.
 
 ## 8. When in doubt
 
-Run `homelab mcp search_docs <query>` or `homelab mcp get_host <name>`.
+Use MCP tools: `search_knowledge <query>` for narrative context,
-The clone is the fallback; MCP is the index.
+`get_entity <slug>` for structured data, `get_entity_knowledge <slug>` for
+everything linked to an entity. The clone is the fallback; MCP is the index.

README.md

@@ -108,7 +108,7 @@ seeds/              Bootstrap YAML (ontology, inventory, policy)
 compose/            Dockerfiles + Caddy config
 scripts/            Deploy, watchdog, verification, rollback
 hermes/             Hermes config, persona, skills
-knowledge/wiki/     Narrative documentation (containers, hosts, infrastructure)
+archive/knowledge/     Narrative documentation (containers, hosts, infrastructure)
 .agents/            Agent instruction files + skills
 plans/              Design documents
 ```
@@ -119,7 +119,7 @@ See [AGENTS.md](AGENTS.md) for the full orientation. Quick reference:
 
 - **Source of truth:** DB (runtime) then repo (bootstrap + docs)
 - **Mutations:** classify against policy, request approval for `destructive`/`config_mutation`
-- **Wiki:** files under `knowledge/wiki/`, changelog at bottom of each page
+- **Wiki:** files under `archive/knowledge/`, changelog at bottom of each page
 - **Secrets:** Infisical (primary) or SOPS (fallback) — never hardcode
 
 ## Related

bootstrap.sh

@@ -18,7 +18,7 @@
 #   - OS is Linux or macOS
 #   - git, age, sops are installed
 #   - at least one mesh (netbird OR tailscale) is connected
-#   - this host has an `hosts/<hostname>.yaml` entry in the repo (or refuses)
+#   - this host has an `inventory.yaml` entry in the repo (or refuses)
 
 set -euo pipefail
 

scripts/cutover-checklist.md

@@ -39,4 +39,4 @@ Status: [x] = done, [ ] = pending
 
 - [ ] Remove Gitea webhooks for apps/105 (ids 10, 11) from `dtoro/Homelab-Docs`
 - [ ] Archive apps/105 LXC (keep for 30 days, then destroy)
-- [x] Update `knowledge/wiki/infrastructure/auto-deploy.md` — apps/105 entries marked deprecated
+- [x] Update auto-deploy docs — apps/105 entries marked deprecated

tools/setup-hermes-soul.sh

@@ -48,7 +48,7 @@ fi
 ## Source of truth
 
 The homelab-context repo at `/opt/homelab-context/` is the single source of truth for:
-- Fleet topology (`inventory.yaml`, `hosts/*.yaml`)
+- Fleet topology (`inventory.yaml`, `inventory.yaml`)
 - Service endpoints and credentials
 - Agent behaviour and conventions