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-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.