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

Generated with SWE-Agent.ai

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

codeagent-wrapper/internal/executor/parallel_config.go

@@ -75,6 +75,12 @@ func ParseParallelConfig(data []byte) (*ParallelConfig, error) {
 					continue
 				}
 				task.SkipPermissions = config.ParseBoolFlag(value, false)
+			case "worktree":
+				if value == "" {
+					task.Worktree = true
+					continue
+				}
+				task.Worktree = config.ParseBoolFlag(value, false)
 			case "dependencies":
 				for _, dep := range strings.Split(value, ",") {
 					dep = strings.TrimSpace(dep)