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)

scripts/cutover-checklist.md

@@ -39,4 +39,4 @@ Status: [x] = done, [ ] = pending
 
 - [ ] Remove Gitea webhooks for apps/105 (ids 10, 11) from `dtoro/Homelab-Docs`
 - [ ] Archive apps/105 LXC (keep for 30 days, then destroy)
-- [x] Update `knowledge/wiki/infrastructure/auto-deploy.md` — apps/105 entries marked deprecated
+- [x] Update auto-deploy docs — apps/105 entries marked deprecated