docs: reshape runbooks into .agents/skills/<name>/SKILL.md (phase 4)

Problem: runbooks are agent-executable procedures but lived at the repo root,
separate from the other agent instruction now under .agents/.

Change:
- Move runbooks/<name>.md -> .agents/skills/<name>/SKILL.md (folder per skill,
  matching the wiki-hq skills layout). Frontmatter (name, risk_class, inputs,
  verification, docs_update_checklist, transition) preserved.
- Rewrite links (inbound from plans; between-skill siblings) via the move map.
- Update prose references in AGENTS.md, HERMES.md, .agents/OIKOS.md, and the
  operations schema; fix a pre-existing stale link to operations/commands.md.

No code consumed runbooks/ by path, so nothing else changes.

Verification: all SKILL.md frontmatter parses with valid risk_class; every
lifecycle transition resolves to an oikos/ontology.yaml state; broken-link
count 127 -> 126 (fixed one, introduced none).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

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

@@ -0,0 +1,35 @@
+---
+name: lifecycle-deprecate-node
+risk_class: config_mutation
+inputs: [node_name, replacement_node_or_reason]
+verification: "homelab node <name> relations — 'affected by' must be empty before completing"
+docs_update_checklist: [doc_page_deprecation_note]
+transition: "active -> deprecated"
+---
+
+# Lifecycle: deprecate a node
+
+Per [oikos/ontology.yaml](../../../oikos/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`
+lists `new-inbound-edges` as refused going forward.
+
+1. Set `state: deprecated` on the node.
+2. `homelab node <name> relations` — read `affected_by`. Every entry
+   there is something still relying on this node.
+3. Migrate or retire each dependent one at a time (point its `backend`/
+   `config_repo`/ingress route elsewhere, or deprecate it too if it's
+   being retired alongside).
+4. Re-run `homelab node <name> relations` after each dependent is moved.
+   The transition to `destroyed` is only safe once `affected_by` is
+   empty — check this every time, don't assume from memory.
+5. Note the deprecation on the doc page: reason, replacement (if any),
+   date.
+
+If step 2 shows dependents you didn't expect, stop and investigate
+before proceeding — that's exactly the kind of drift the Week-3 detector
+will catch automatically, but until then this manual check is the gate.
+
+Next (once `affected_by` is empty):
+[lifecycle-destroy-node.md](../lifecycle-destroy-node/SKILL.md).