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>

codeagent-wrapper/internal/config/config.go

@@ -26,6 +26,7 @@ type Config struct {
 	MaxParallelWorkers int
 	AllowedTools       []string
 	DisallowedTools    []string
+	Worktree           bool // Execute in a new git worktree
 }
 
 // EnvFlagEnabled returns true when the environment variable exists and is not