fix(3347): clear CI gates raised by initial commit

- docs/CONFIGURATION.md: document graphify.auto_update key (config-schema-docs-parity)
- hooks/gsd-check-update-worker.js: add gsd-graphify-update.sh to MANAGED_HOOKS (managed-hooks)
- agents/gsd-planner.md + gsd-phase-researcher.md: slim auto-update awareness block to
  a one-line @-reference; extract full instructions to a new reference file
- get-shit-done/references/planner-graphify-auto-update.md: new reference with the
  status-file schema, the four annotation cases (running/failed/ok-current/ok-stale),
  and interaction with the existing stale-mtime annotation
- docs/INVENTORY.md: References (60 → 61 shipped) + row for new reference; regenerate
  docs/INVENTORY-MANIFEST.json via gen-inventory-manifest.cjs

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

docs/INVENTORY-MANIFEST.json

@@ -224,6 +224,7 @@
       "planner-antipatterns.md",
       "planner-chunked.md",
       "planner-gap-closure.md",
+      "planner-graphify-auto-update.md",
       "planner-human-verify-mode.md",
       "planner-mvp-mode.md",
       "planner-reviews.md",