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)

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
 
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