feat: add worktree support and refactor do skill to Python

- Add worktree module for git worktree management
- Refactor do skill scripts from shell to Python for better maintainability
- Add install.py for do skill installation
- Update stop-hook to Python implementation
- Enhance executor with additional configuration options
- Update CLAUDE.md with first-principles thinking guidelines

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Co-Authored-By: SWE-Agent.ai <noreply@swe-agent.ai>

skills/do/hooks/hooks.json

@@ -1,12 +1,12 @@
 {
-  "description": "do loop hook for 7-phase workflow",
+  "description": "do loop hook for 5-phase workflow",
   "hooks": {
     "Stop": [
       {
         "hooks": [
           {
             "type": "command",
-            "command": "${CLAUDE_PLUGIN_ROOT}/hooks/stop-hook.sh"
+            "command": "python3 ${CLAUDE_PLUGIN_ROOT}/hooks/stop-hook.py"
           }
         ]
       }