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/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