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/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.