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/app/cli.go

@@ -30,6 +30,7 @@ type cliOptions struct {
 	Agent           string
 	PromptFile      string
 	SkipPermissions bool
+	Worktree        bool
 
 	Parallel   bool
 	FullOutput bool
@@ -136,6 +137,7 @@ func addRootFlags(fs *pflag.FlagSet, opts *cliOptions) {
 
 	fs.BoolVar(&opts.SkipPermissions, "skip-permissions", false, "Skip permissions prompts (also via CODEAGENT_SKIP_PERMISSIONS)")
 	fs.BoolVar(&opts.SkipPermissions, "dangerously-skip-permissions", false, "Alias for --skip-permissions")
+	fs.BoolVar(&opts.Worktree, "worktree", false, "Execute in a new git worktree (auto-generates task ID)")
 }
 
 func newVersionCommand(name string) *cobra.Command {
@@ -350,6 +352,7 @@ func buildSingleConfig(cmd *cobra.Command, args []string, rawArgv []string, opts
 		MaxParallelWorkers: config.ResolveMaxParallelWorkers(),
 		AllowedTools:       resolvedAllowedTools,
 		DisallowedTools:    resolvedDisallowedTools,
+		Worktree:           opts.Worktree,
 	}
 
 	if args[0] == "resume" {
@@ -653,6 +656,7 @@ func runSingleMode(cfg *Config, name string) int {
 		ReasoningEffort: cfg.ReasoningEffort,
 		Agent:           cfg.Agent,
 		SkipPermissions: cfg.SkipPermissions,
+		Worktree:        cfg.Worktree,
 		AllowedTools:    cfg.AllowedTools,
 		DisallowedTools: cfg.DisallowedTools,
 		UseStdin:        useStdin,

codeagent-wrapper/internal/app/main_test.go

@@ -1616,6 +1616,60 @@ do something`
 	}
 }
 
+func TestParallelParseConfig_Worktree(t *testing.T) {
+	input := `---TASK---
+id: task-1
+worktree: true
+---CONTENT---
+do something`
+
+	cfg, err := parseParallelConfig([]byte(input))
+	if err != nil {
+		t.Fatalf("parseParallelConfig() unexpected error: %v", err)
+	}
+	if len(cfg.Tasks) != 1 {
+		t.Fatalf("expected 1 task, got %d", len(cfg.Tasks))
+	}
+	task := cfg.Tasks[0]
+	if !task.Worktree {
+		t.Fatalf("Worktree = %v, want true", task.Worktree)
+	}
+}
+
+func TestParallelParseConfig_WorktreeBooleanValue(t *testing.T) {
+	tests := []struct {
+		name  string
+		value string
+		want  bool
+	}{
+		{"true", "true", true},
+		{"1", "1", true},
+		{"yes", "yes", true},
+		{"false", "false", false},
+		{"0", "0", false},
+		{"no", "no", false},
+		{"empty", "", true},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			input := fmt.Sprintf(`---TASK---
+id: task-1
+worktree: %s
+---CONTENT---
+do something`, tt.value)
+
+			cfg, err := parseParallelConfig([]byte(input))
+			if err != nil {
+				t.Fatalf("parseParallelConfig() unexpected error: %v", err)
+			}
+			if cfg.Tasks[0].Worktree != tt.want {
+				t.Fatalf("Worktree = %v, want %v for value %q", cfg.Tasks[0].Worktree, tt.want, tt.value)
+			}
+		})
+	}
+}
+
 func TestParallelParseConfig_EmptySessionID(t *testing.T) {
 	input := `---TASK---
 id: task-1