refactor: flatten skills/ and adopt Agent Plugins 1.0

The Agent Plugins standard reads only the immediate children of
skills/ and cannot be pointed elsewhere, so a bucketed tree is
invisible to every conformant client.

Rather than generate a flat copy of the repo into a package
directory — a builder, a validator, an allowlist, a drift CI job,
and every skill committed twice — remove the buckets.

- skills/ is flat and holds exactly the promoted 25
- in-progress/ -> drafts/, misc/ -> extras/, deprecated/ deleted
- new root plugin.json (Agent Plugins 1.0)
- .claude-plugin/plugin.json loses its 25-entry skills array
- docs/ keeps its category folders; it is now the only place a
  skill's category lives

Reasoning in .agents/adr/0003.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

.github/workflows/release.yml

@@ -26,6 +26,9 @@ jobs:
       - name: Install dependencies
         run: npm ci
 
+      - name: Check plugin manifest versions
+        run: npm run check-plugin-version
+
       - name: Create Version Pull Request
         uses: changesets/action@v1
         with: