refactor: migrate plugin structure from .claude-plugin to project root

Restructure plugin to follow Claude Code official documentation:
- Move TypeScript files from .claude-plugin/* to project root
- Create Markdown command files in commands/
- Update plugin.json to reference ./commands/*.md
- Add comprehensive plugin installation guide

Changes:
- Commands: pm.md, research.md, index-repo.md (new Markdown format)
- TypeScript: pm/, research/, index/ moved to root
- Hooks: hooks/hooks.json moved to root
- Documentation: PLUGIN_INSTALL.md, updated CLAUDE.md, Makefile

Note: This commit represents transition state. Original TypeScript-based
execution system was replaced with Markdown commands. Further redesign
needed to properly integrate Skills and Hooks per official docs.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.claude-plugin/plugin.json

@@ -1,38 +1,18 @@
 {
   "name": "pm-agent",
-  "version": "2.0.0",
-  "description": "PM Agent - Auto-activating orchestrator with hot reload support",
-  "author": "SuperClaude Team",
-  "main": "pm/index.ts",
-  "commands": [
-    {
-      "name": "pm",
-      "path": "pm/index.ts",
-      "description": "Activate PM Agent with confidence-driven workflow (auto-starts via hooks)"
-    },
-    {
-      "name": "research",
-      "path": "research/index.ts",
-      "description": "Deep web research with adaptive planning and intelligent search"
-    },
-    {
-      "name": "index-repo",
-      "path": "index/index.ts",
-      "description": "Create repository structure index for fast context loading (94% token reduction)"
-    }
-  ],
-  "skills": [
-    {
-      "name": "confidence_check",
-      "path": "pm/confidence.ts",
-      "description": "Pre-implementation confidence assessment (≥90% required, Precision/Recall 1.0)"
-    }
-  ],
-  "hooks": {
-    "path": "hooks/hooks.json",
-    "description": "SessionStart auto-activation: /pm runs automatically on session start"
+  "version": "2.1.0",
+  "description": "PM Agent - Confidence-driven orchestrator with deep research and repository indexing",
+  "author": {
+    "name": "SuperClaude Team"
   },
-  "engines": {
-    "node": ">=18.0.0"
-  }
+  "homepage": "https://github.com/kazukixjp/superclaude",
+  "repository": "https://github.com/kazukixjp/superclaude",
+  "license": "MIT",
+  "keywords": ["pm-agent", "confidence-check", "research", "indexing"],
+  "commands": [
+    "./commands/pm.md",
+    "./commands/research.md",
+    "./commands/index-repo.md"
+  ],
+  "hooks": "./hooks/hooks.json"
 }