sync AGENTS.md tool list with MCP server (63 tools); fix 7 stale references in .agents/

.agents/skills/lifecycle-destroy-node/SKILL.md

@@ -36,8 +36,9 @@ ledger entry.
 6. Update the entity's `state` to `destroyed` in `seeds/inventory.yaml`
    (or move it to an `archaeology:`-style section if the schema still has
    one) — `pve_id`, `destroyed` date, `reason` — then `oikos seed` to
-   ingest. Add a row to `containers/index.md` "Recently destroyed" table
-   (kept for human-readable browsing alongside the structured data).
+ingest. Add a row to the legacy `archive/knowledge/containers/index.md`
+    "Recently destroyed" table (kept for human-readable browsing
+    alongside the structured data in the DB).
 7. No manual ledger step — mutations through the API are recorded
    automatically in the `audit_log` table (MCP `get_audit_trail`,
    `get_change_history`). The old `oikos/ledger.py append` was retired