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/marketplace.json

@@ -1,12 +1,15 @@
 {
   "name": "superclaude-local",
   "description": "Local development marketplace for SuperClaude plugins",
+  "owner": {
+    "name": "SuperClaude Team"
+  },
   "plugins": [
     {
       "name": "pm-agent",
-      "path": ".",
-      "version": "1.0.0",
-      "description": "Project Manager Agent with 90% confidence checks and zero-footprint memory"
+      "source": "./pm-agent",
+      "version": "2.1.0",
+      "description": "PM Agent - Confidence-driven orchestrator with deep research and repository indexing"
     }
   ]
 }