Add main_branch config key for branch protection and base branch selection

README.md

@@ -239,6 +239,7 @@ project/
 ```yaml
 version: 1
 git_dir: .bare
+main_branch: main
 editor: cursor
 setup:
   - "cp .env.example .env"
@@ -256,6 +257,7 @@ parallel_teardown:
 |-------|-------------|---------|
 | `version` | Config version | `1` |
 | `git_dir` | Path to bare repository | `.bare` |
+| `main_branch` | Primary branch (protected from removal, used as base for new branches) | `main` |
 | `editor` | Preferred editor binary name | (auto-detect) |
 | `setup` | Commands to run sequentially after creating a worktree | `[]` |
 | `parallel_setup` | Commands to run concurrently after serial setup hooks | `[]` |

cmd/add.go

@@ -96,7 +96,8 @@ func runAdd(cmd *cobra.Command, args []string) error {
 			return err
 		}
 	} else {
-		if err := runner.WorktreeAddNew(ctx, worktreePath, branch); err != nil {
+		startPoint := runner.ResolveStartPoint(ctx, cfg.MainBranchOrDefault())
+		if err := runner.WorktreeAddNew(ctx, worktreePath, branch, startPoint); err != nil {
 			return err
 		}
 	}

cmd/agents.go

@@ -159,6 +159,7 @@ After wt init (existing repo):
     version: 1
     git_dir: .bare                    # .bare for clone, .git for init
     worktree_dir: worktrees
+    main_branch: main                 # auto-detected at clone/init
     editor: cursor
     setup:
       - "npm install"
@@ -173,6 +174,7 @@ Fields:
 - version: Config version (always 1)
 - git_dir: Path to git directory (.bare for cloned, .git for initialized)
 - worktree_dir: Directory for worktrees (default: worktrees)
+- main_branch: Primary branch, protected from removal and used as base for new branches (default: main)
 - editor: Preferred editor binary name (default: auto-detect)
 - setup: Commands run sequentially after creating a worktree
 - parallel_setup: Commands run concurrently after setup completes

cmd/claude.go

@@ -158,7 +158,8 @@ func runClaudeHookWorktreeCreate(cmd *cobra.Command, _ []string) error {
 			return fmt.Errorf("worktree add failed: %w", err)
 		}
 	} else {
-		if err := runner.WorktreeAddNew(ctx, worktreePath, branch); err != nil {
+		startPoint := runner.ResolveStartPoint(ctx, cfg.MainBranchOrDefault())
+		if err := runner.WorktreeAddNew(ctx, worktreePath, branch, startPoint); err != nil {
 			return fmt.Errorf("worktree add (new branch) failed: %w", err)
 		}
 	}

cmd/clone.go

@@ -72,8 +72,17 @@ func runClone(cmd *cobra.Command, args []string) error {
 		return err
 	}
 
+	// Detect the remote's default branch
+	ui.Step("Detecting default branch")
+	detectedBranch, err := runner.GetDefaultBranch(ctx)
+	if err != nil {
+		ui.Warning("Could not detect default branch, defaulting to 'main'")
+		detectedBranch = config.DefaultMainBranch
+	}
+
 	// Create scaffold directories
 	cfg := config.DefaultConfig()
+	cfg.MainBranch = detectedBranch
 	ui.Step("Creating project scaffold")
 	if err := project.CreateScaffold(projectRoot, &cfg, dry); err != nil {
 		return err
@@ -90,7 +99,7 @@ func runClone(cmd *cobra.Command, args []string) error {
 	if dry {
 		ui.DryRunNotice("write " + filepath.Join(projectRoot, config.ConfigFileName))
 	} else {
-		if err := config.WriteAnnotated(projectRoot); err != nil {
+		if err := config.WriteAnnotatedWithValues(projectRoot, &cfg); err != nil {
 			return err
 		}
 	}

cmd/init.go

@@ -6,6 +6,7 @@ import (
 	"path/filepath"
 
 	"github.com/bkildow/wt-cli/internal/config"
+	"github.com/bkildow/wt-cli/internal/git"
 	"github.com/bkildow/wt-cli/internal/project"
 	"github.com/bkildow/wt-cli/internal/ui"
 	"github.com/spf13/cobra"
@@ -49,14 +50,23 @@ func runInit(cmd *cobra.Command, args []string) error {
 	cfg.WorktreeDir = ".worktrees"
 	cfg.SharedDir = ".worktrees/shared"
 
+	// Detect the repository's default branch
+	gitDir := filepath.Join(projectRoot, cfg.GitDir)
+	initRunner := git.NewRunner(gitDir, dry)
+	detectedBranch, err := initRunner.GetDefaultBranch(cmd.Context())
+	if err != nil {
+		ui.Warning("Could not detect default branch, defaulting to 'main'")
+		detectedBranch = config.DefaultMainBranch
+	}
+	cfg.MainBranch = detectedBranch
+
 	// Create scaffold directories
 	ui.Step("Creating project scaffold")
 	if err := project.CreateScaffold(projectRoot, &cfg, dry); err != nil {
 		return err
 	}
 
 	// Configure local git excludes for wt-managed files
-	gitDir := filepath.Join(projectRoot, cfg.GitDir)
 	ui.Step("Configuring local git excludes")
 	if err := project.EnsureGitExclude(gitDir, dry); err != nil {
 		return err

cmd/prune.go

@@ -34,10 +34,7 @@ func runPrune(cmd *cobra.Command, args []string) error {
 	cwd, _ := os.Getwd()
 	runner := git.NewRunner(project.GitDirPath(projectRoot, cfg), IsDryRun())
 
-	defaultBranch, err := runner.GetDefaultBranch(ctx)
-	if err != nil {
-		return err
-	}
+	defaultBranch := cfg.MainBranchOrDefault()
 
 	worktrees, err := runner.WorktreeList(ctx)
 	if err != nil {

cmd/remove.go

@@ -79,6 +79,11 @@ func runRemove(cmd *cobra.Command, args []string) error {
 		}
 	}
 
+	// Protect the main branch from accidental removal.
+	if selected.Branch == cfg.MainBranchOrDefault() {
+		return fmt.Errorf("cannot remove the main branch worktree (%s)", selected.Branch)
+	}
+
 	force, _ := cmd.Flags().GetBool("force")
 
 	if !force {

internal/config/config.go

@@ -16,6 +16,7 @@ const (
 	DefaultGitDir      = ".bare"
 	DefaultWorktreeDir = "worktrees"
 	DefaultSharedDir   = "shared"
+	DefaultMainBranch  = "main"
 )
 
 var (
@@ -28,6 +29,7 @@ type Config struct {
 	GitDir           string   `yaml:"git_dir"`
 	WorktreeDir      string   `yaml:"worktree_dir"`
 	SharedDir        string   `yaml:"shared_dir"`
+	MainBranch       string   `yaml:"main_branch,omitempty"`
 	Setup            []string `yaml:"setup,omitempty"`
 	ParallelSetup    []string `yaml:"parallel_setup,omitempty"`
 	Teardown         []string `yaml:"teardown,omitempty"`
@@ -36,6 +38,14 @@ type Config struct {
 	Editor           string   `yaml:"editor,omitempty"`
 }
 
+// MainBranchOrDefault returns the configured main branch, falling back to DefaultMainBranch.
+func (c *Config) MainBranchOrDefault() string {
+	if c.MainBranch != "" {
+		return c.MainBranch
+	}
+	return DefaultMainBranch
+}
+
 func DefaultConfig() Config {
 	return Config{
 		Version:     1,
@@ -116,6 +126,13 @@ func renderAnnotatedConfig(cfg *Config) string {
 		fmt.Fprintf(&b, "shared_dir: %s\n", DefaultSharedDir)
 	}
 
+	b.WriteString("\n# The primary branch of the repository (used as base for new branches, protected from removal)\n")
+	if cfg != nil && cfg.MainBranch != "" {
+		fmt.Fprintf(&b, "main_branch: %s\n", cfg.MainBranch)
+	} else {
+		b.WriteString("# main_branch: main\n")
+	}
+
 	b.WriteString("\n# Editor for 'wt open' (e.g. cursor, code, zed)\n")
 	b.WriteString("# Falls back to $EDITOR, then auto-detects\n")
 	if cfg != nil && cfg.Editor != "" {

internal/config/config_test.go

@@ -193,6 +193,11 @@ func TestWriteAnnotated(t *testing.T) {
 		t.Error("missing worktree_dir default")
 	}
 
+	// main_branch should be commented out
+	if !strings.Contains(content, "# main_branch: main") {
+		t.Error("main_branch should be commented out as example")
+	}
+
 	// Optional fields should be commented out
 	if !strings.Contains(content, "# editor: cursor") {
 		t.Error("editor should be commented out as example")
@@ -233,6 +238,7 @@ func TestWriteAnnotatedWithValues(t *testing.T) {
 		Version:     1,
 		GitDir:      ".bare",
 		WorktreeDir: "trees",
+		MainBranch:  "develop",
 		Setup:       []string{"npm install", "cp .env.example .env"},
 		Teardown:    []string{"docker compose down"},
 		Editor:      "cursor",
@@ -253,6 +259,14 @@ func TestWriteAnnotatedWithValues(t *testing.T) {
 		t.Error("missing header comment")
 	}
 
+	// main_branch should be uncommented with existing value
+	if !strings.Contains(content, "main_branch: develop") {
+		t.Error("missing main_branch value")
+	}
+	if strings.Contains(content, "# main_branch:") {
+		t.Error("main_branch should not be commented out when value exists")
+	}
+
 	// Editor should be uncommented with existing value
 	if !strings.Contains(content, "editor: cursor") {
 		t.Error("missing editor value")
@@ -339,6 +353,83 @@ func TestWriteAnnotatedWithGitDirDotGit(t *testing.T) {
 	}
 }
 
+func TestMainBranchOrDefault(t *testing.T) {
+	t.Run("empty returns default", func(t *testing.T) {
+		cfg := Config{}
+		if got := cfg.MainBranchOrDefault(); got != DefaultMainBranch {
+			t.Errorf("MainBranchOrDefault() = %q, want %q", got, DefaultMainBranch)
+		}
+	})
+	t.Run("set value is returned", func(t *testing.T) {
+		cfg := Config{MainBranch: "develop"}
+		if got := cfg.MainBranchOrDefault(); got != "develop" {
+			t.Errorf("MainBranchOrDefault() = %q, want %q", got, "develop")
+		}
+	})
+}
+
+func TestLoadConfigWithMainBranch(t *testing.T) {
+	dir := t.TempDir()
+	content := `version: 1
+git_dir: .bare
+main_branch: develop
+`
+	if err := os.WriteFile(filepath.Join(dir, ConfigFileName), []byte(content), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	cfg, err := Load(dir)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if cfg.MainBranch != "develop" {
+		t.Errorf("main_branch = %q, want %q", cfg.MainBranch, "develop")
+	}
+	if cfg.MainBranchOrDefault() != "develop" {
+		t.Errorf("MainBranchOrDefault() = %q, want %q", cfg.MainBranchOrDefault(), "develop")
+	}
+}
+
+func TestLoadConfigWithoutMainBranch(t *testing.T) {
+	dir := t.TempDir()
+	content := `version: 1
+git_dir: .bare
+`
+	if err := os.WriteFile(filepath.Join(dir, ConfigFileName), []byte(content), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	cfg, err := Load(dir)
+	if err != nil {
+		t.Fatalf("unexpected error: %v", err)
+	}
+	if cfg.MainBranch != "" {
+		t.Errorf("main_branch = %q, want empty (backward compat)", cfg.MainBranch)
+	}
+	if cfg.MainBranchOrDefault() != DefaultMainBranch {
+		t.Errorf("MainBranchOrDefault() = %q, want %q", cfg.MainBranchOrDefault(), DefaultMainBranch)
+	}
+}
+
+func TestSaveAndLoadMainBranchRoundTrip(t *testing.T) {
+	dir := t.TempDir()
+	original := &Config{
+		Version:    1,
+		GitDir:     ".bare",
+		MainBranch: "develop",
+	}
+	if err := original.Save(dir); err != nil {
+		t.Fatalf("save error: %v", err)
+	}
+	loaded, err := Load(dir)
+	if err != nil {
+		t.Fatalf("load error: %v", err)
+	}
+	if loaded.MainBranch != "develop" {
+		t.Errorf("main_branch = %q, want %q", loaded.MainBranch, "develop")
+	}
+}
+
 func TestYamlQuote(t *testing.T) {
 	tests := []struct {
 		input string

internal/git/git.go

@@ -28,7 +28,7 @@ type Git interface {
 	ListRemoteBranches(ctx context.Context) ([]string, error)
 	HasRemoteBranch(ctx context.Context, branch string) (bool, error)
 	WorktreeAdd(ctx context.Context, path, branch string) error
-	WorktreeAddNew(ctx context.Context, path, branch string) error
+	WorktreeAddNew(ctx context.Context, path, branch, baseBranch string) error
 	WorktreeRemove(ctx context.Context, path string, force bool) error
 	WorktreeList(ctx context.Context) ([]WorktreeInfo, error)
 	WorktreePrune(ctx context.Context) error
@@ -155,8 +155,8 @@ func (r *Runner) WorktreeAdd(ctx context.Context, path, branch string) error {
 	return err
 }
 
-func (r *Runner) WorktreeAddNew(ctx context.Context, path, branch string) error {
-	_, err := r.Run(ctx, "worktree", "add", "--relative-paths", "-b", branch, path, "HEAD")
+func (r *Runner) WorktreeAddNew(ctx context.Context, path, branch, baseBranch string) error {
+	_, err := r.Run(ctx, "worktree", "add", "--relative-paths", "-b", branch, path, baseBranch)
 	return err
 }
 
@@ -298,6 +298,19 @@ func (r *Runner) GetDefaultBranch(ctx context.Context) (string, error) {
 	return "", fmt.Errorf("could not determine default branch")
 }
 
+// ResolveStartPoint finds a valid git ref for the given branch name.
+// It tries origin/<branch> first (for bare repos), then the local branch,
+// and falls back to HEAD if neither exists.
+func (r *Runner) ResolveStartPoint(ctx context.Context, branch string) string {
+	if _, err := r.Run(ctx, "rev-parse", "--verify", "origin/"+branch); err == nil {
+		return "origin/" + branch
+	}
+	if _, err := r.Run(ctx, "rev-parse", "--verify", branch); err == nil {
+		return branch
+	}
+	return "HEAD"
+}
+
 func (r *Runner) WorktreePrune(ctx context.Context) error {
 	_, err := r.Run(ctx, "worktree", "prune")
 	return err

internal/git/git_test.go

@@ -130,7 +130,7 @@ func TestDryRunMode(t *testing.T) {
 	}
 
 	// WorktreeAddNew
-	if err := runner.WorktreeAddNew(ctx, "/tmp/wt", "feature-x"); err != nil {
+	if err := runner.WorktreeAddNew(ctx, "/tmp/wt", "feature-x", "main"); err != nil {
 		t.Errorf("dry-run WorktreeAddNew returned error: %v", err)
 	}