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Root inventory.yaml (618-line Python-era file superseded 2026-07-07 by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.

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`
-describe `bin/homelab`, `oikos/cards/`, `oikos/ledger.py`, root
-`inventory.yaml`, `knowledge/sources/`, `get_page`/`search_docs` MCP tools —
-none of which exist. They contradict AGENTS.md §"Source of truth" and ADR
-0003. **These need a full rewrite** (deferred — substantial; tracked as
-recommendation R5).
+`.agents/domains/knowledge/schema.md` and `.agents/shared/llm-wiki.md` previously described
+`bin/homelab`, `oikos/cards/`, `oikos/ledger.py`, root `inventory.yaml`, `knowledge/sources/`,
+`get_page`/`search_docs` MCP tools — none of which exist. **Rewritten** for the DB-native model
+(ADR 0003): DB is the single source of truth for both structured data and narrative knowledge;
+`seeds/*.yaml` are the bootstrap+DR manifests; `archive/knowledge/` is the frozen legacy wiki;
+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
-`seeds/inventory.yaml` on 2026-07-07. Multiple `.agents/` docs still treat bare
-`inventory.yaml` as the kernel source of truth. **Delete or mark explicitly
-deprecated** (deferred — touches `.agents/shared/*` and `.agents/domains/*`
-which need the substrate rewrite in R5 anyway).
+20387-byte Python-era file superseded by `seeds/inventory.yaml` on 2026-07-07. **Replaced with a
+deprecation stub** pointing to `seeds/inventory.yaml` and the DB (ADR 0003). Kept as a stub rather
+than deleted because AGENTS.md §1/§2 still point clients at `/opt/homelab-context/inventory.yaml`
+(the on-client clone path); full path reconciliation is R13. `.agents/shared/*` and
+`.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 |