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>

.claude-plugin/plugin.json

@@ -17,32 +17,5 @@
     "grilling",
     "domain-modeling",
     "productivity"
-  ],
-  "skills": [
-    "./skills/engineering/ask-matt",
-    "./skills/engineering/diagnosing-bugs",
-    "./skills/engineering/grill-with-docs",
-    "./skills/engineering/triage",
-    "./skills/engineering/improve-codebase-architecture",
-    "./skills/engineering/setup-matt-pocock-skills",
-    "./skills/engineering/tdd",
-    "./skills/engineering/to-spec",
-    "./skills/engineering/to-tickets",
-    "./skills/engineering/wayfinder",
-    "./skills/engineering/implement",
-    "./skills/engineering/prototype",
-    "./skills/engineering/research",
-    "./skills/engineering/domain-modeling",
-    "./skills/engineering/codebase-design",
-    "./skills/engineering/code-review",
-    "./skills/engineering/resolving-merge-conflicts",
-    "./skills/engineering/wizard",
-    "./skills/productivity/grill-me",
-    "./skills/productivity/grilling",
-    "./skills/productivity/handoff",
-    "./skills/productivity/teach",
-    "./skills/productivity/to-questionnaire",
-    "./skills/productivity/wait-what",
-    "./skills/productivity/writing-for-agents"
   ]
 }