diff --git a/internal/cmd/crew.go b/internal/cmd/crew.go
index 59b328d3..4b318d9c 100644
--- a/internal/cmd/crew.go
+++ b/internal/cmd/crew.go
@@ -482,6 +482,9 @@ func runCrewAt(cmd *cobra.Command, args []string) error {
 		return fmt.Errorf("getting crew worker: %w", err)
 	}
 
+	// Ensure crew workspace is on main branch (persistent roles should not use feature branches)
+	ensureMainBranch(worker.ClonePath, fmt.Sprintf("Crew workspace %s/%s", r.Name, name))
+
 	// If --no-tmux, just print the path
 	if crewNoTmux {
 		fmt.Println(worker.ClonePath)
@@ -1137,3 +1140,45 @@ func runCrewPristine(cmd *cobra.Command, args []string) error {
 
 	return nil
 }
+
+// ensureMainBranch checks if a git directory is on main branch.
+// If not, warns the user and offers to switch.
+// Returns true if on main (or switched to main), false if user declined.
+func ensureMainBranch(dir, roleName string) bool {
+	g := git.NewGit(dir)
+
+	branch, err := g.CurrentBranch()
+	if err != nil {
+		// Not a git repo or other error, skip check
+		return true
+	}
+
+	if branch == "main" || branch == "master" {
+		return true
+	}
+
+	// Warn about wrong branch
+	fmt.Printf("\n%s %s is on branch '%s', not main\n",
+		style.Warning.Render("⚠"),
+		roleName,
+		branch)
+	fmt.Println("  Persistent roles should work on main to avoid orphaned work.")
+	fmt.Println()
+
+	// Auto-switch to main
+	fmt.Printf("  Switching to main...\n")
+	if err := g.Checkout("main"); err != nil {
+		fmt.Printf("  %s Could not switch to main: %v\n", style.Error.Render("✗"), err)
+		fmt.Println("  Please manually run: git checkout main && git pull")
+		return false
+	}
+
+	// Pull latest
+	if err := g.Pull("origin", "main"); err != nil {
+		fmt.Printf("  %s Pull failed (continuing anyway): %v\n", style.Warning.Render("⚠"), err)
+	} else {
+		fmt.Printf("  %s Switched to main and pulled latest\n", style.Success.Render("✓"))
+	}
+
+	return true
+}
diff --git a/internal/cmd/doctor.go b/internal/cmd/doctor.go
index 2cabafa6..db42dfef 100644
--- a/internal/cmd/doctor.go
+++ b/internal/cmd/doctor.go
@@ -57,6 +57,8 @@ func runDoctor(cmd *cobra.Command, args []string) error {
 	d.Register(doctor.NewBeadsDatabaseCheck())
 	d.Register(doctor.NewOrphanSessionCheck())
 	d.Register(doctor.NewOrphanProcessCheck())
+	d.Register(doctor.NewBranchCheck())
+	d.Register(doctor.NewBeadsSyncOrphanCheck())
 
 	// Run checks
 	var report *doctor.Report
diff --git a/internal/doctor/branch_check.go b/internal/doctor/branch_check.go
new file mode 100644
index 00000000..3f11a6dd
--- /dev/null
+++ b/internal/doctor/branch_check.go
@@ -0,0 +1,324 @@
+package doctor
+
+import (
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+)
+
+// BranchCheck detects persistent roles (crew, witness, refinery) that are
+// not on the main branch. Long-lived roles should work directly on main
+// to avoid orphaned work and branch decay.
+type BranchCheck struct {
+	FixableCheck
+	offMainDirs []string // Cached during Run for use in Fix
+}
+
+// NewBranchCheck creates a new branch check.
+func NewBranchCheck() *BranchCheck {
+	return &BranchCheck{
+		FixableCheck: FixableCheck{
+			BaseCheck: BaseCheck{
+				CheckName:        "persistent-role-branches",
+				CheckDescription: "Detect persistent roles not on main branch",
+			},
+		},
+	}
+}
+
+// Run checks if persistent role directories are on main branch.
+func (c *BranchCheck) Run(ctx *CheckContext) *CheckResult {
+	var offMain []string
+	var onMain int
+
+	// Find all persistent role directories
+	dirs := c.findPersistentRoleDirs(ctx.TownRoot)
+
+	for _, dir := range dirs {
+		branch, err := c.getCurrentBranch(dir)
+		if err != nil {
+			// Skip directories that aren't git repos
+			continue
+		}
+
+		if branch == "main" || branch == "master" {
+			onMain++
+		} else {
+			offMain = append(offMain, fmt.Sprintf("%s (on %s)", c.relativePath(ctx.TownRoot, dir), branch))
+		}
+	}
+
+	// Cache for Fix
+	c.offMainDirs = nil
+	for _, dir := range dirs {
+		branch, err := c.getCurrentBranch(dir)
+		if err != nil {
+			continue
+		}
+		if branch != "main" && branch != "master" {
+			c.offMainDirs = append(c.offMainDirs, dir)
+		}
+	}
+
+	if len(offMain) == 0 {
+		if onMain == 0 {
+			return &CheckResult{
+				Name:    c.Name(),
+				Status:  StatusOK,
+				Message: "No persistent role directories found",
+			}
+		}
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: fmt.Sprintf("All %d persistent roles on main branch", onMain),
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("%d persistent role(s) not on main branch", len(offMain)),
+		Details: offMain,
+		FixHint: "Run 'gt doctor --fix' to switch to main, or manually: git checkout main && git pull",
+	}
+}
+
+// Fix switches all off-main directories to main branch.
+func (c *BranchCheck) Fix(ctx *CheckContext) error {
+	if len(c.offMainDirs) == 0 {
+		return nil
+	}
+
+	var lastErr error
+	for _, dir := range c.offMainDirs {
+		// git checkout main
+		cmd := exec.Command("git", "checkout", "main")
+		cmd.Dir = dir
+		if err := cmd.Run(); err != nil {
+			lastErr = fmt.Errorf("%s: %w", dir, err)
+			continue
+		}
+
+		// git pull --rebase
+		cmd = exec.Command("git", "pull", "--rebase")
+		cmd.Dir = dir
+		if err := cmd.Run(); err != nil {
+			// Pull failure is not fatal, just warn
+			continue
+		}
+	}
+
+	return lastErr
+}
+
+// findPersistentRoleDirs finds all directories that should be on main:
+// - <rig>/crew/*
+// - <rig>/witness/rig (if exists)
+// - <rig>/refinery/rig (if exists)
+func (c *BranchCheck) findPersistentRoleDirs(townRoot string) []string {
+	var dirs []string
+
+	// Find all rigs
+	entries, err := os.ReadDir(townRoot)
+	if err != nil {
+		return dirs
+	}
+
+	for _, entry := range entries {
+		if !entry.IsDir() {
+			continue
+		}
+		// Skip non-rig directories
+		name := entry.Name()
+		if name == "mayor" || name == ".beads" || strings.HasPrefix(name, ".") {
+			continue
+		}
+
+		rigPath := filepath.Join(townRoot, name)
+
+		// Check if this looks like a rig (has crew/, polecats/, witness/, or refinery/)
+		if !c.isRig(rigPath) {
+			continue
+		}
+
+		// Add crew members
+		crewPath := filepath.Join(rigPath, "crew")
+		if crewEntries, err := os.ReadDir(crewPath); err == nil {
+			for _, crew := range crewEntries {
+				if crew.IsDir() && !strings.HasPrefix(crew.Name(), ".") {
+					dirs = append(dirs, filepath.Join(crewPath, crew.Name()))
+				}
+			}
+		}
+
+		// Add witness/rig if exists
+		witnessRig := filepath.Join(rigPath, "witness", "rig")
+		if _, err := os.Stat(witnessRig); err == nil {
+			dirs = append(dirs, witnessRig)
+		}
+
+		// Add refinery/rig if exists
+		refineryRig := filepath.Join(rigPath, "refinery", "rig")
+		if _, err := os.Stat(refineryRig); err == nil {
+			dirs = append(dirs, refineryRig)
+		}
+	}
+
+	return dirs
+}
+
+// isRig checks if a directory looks like a rig.
+func (c *BranchCheck) isRig(path string) bool {
+	markers := []string{"crew", "polecats", "witness", "refinery"}
+	for _, marker := range markers {
+		if _, err := os.Stat(filepath.Join(path, marker)); err == nil {
+			return true
+		}
+	}
+	return false
+}
+
+// getCurrentBranch returns the current git branch for a directory.
+func (c *BranchCheck) getCurrentBranch(dir string) (string, error) {
+	cmd := exec.Command("git", "branch", "--show-current")
+	cmd.Dir = dir
+	out, err := cmd.Output()
+	if err != nil {
+		return "", err
+	}
+	return strings.TrimSpace(string(out)), nil
+}
+
+// relativePath returns path relative to base, or the full path if that fails.
+func (c *BranchCheck) relativePath(base, path string) string {
+	rel, err := filepath.Rel(base, path)
+	if err != nil {
+		return path
+	}
+	return rel
+}
+
+// BeadsSyncOrphanCheck detects code changes on beads-sync branch that weren't
+// merged to main. This catches cases where merges lose code changes.
+type BeadsSyncOrphanCheck struct {
+	BaseCheck
+}
+
+// NewBeadsSyncOrphanCheck creates a new beads-sync orphan check.
+func NewBeadsSyncOrphanCheck() *BeadsSyncOrphanCheck {
+	return &BeadsSyncOrphanCheck{
+		BaseCheck: BaseCheck{
+			CheckName:        "beads-sync-orphans",
+			CheckDescription: "Detect orphaned code on beads-sync branch",
+		},
+	}
+}
+
+// Run checks for code differences between main and beads-sync.
+func (c *BeadsSyncOrphanCheck) Run(ctx *CheckContext) *CheckResult {
+	// Find the first rig with a crew member (that has beads-sync branch)
+	crewDirs := c.findCrewDirs(ctx.TownRoot)
+	if len(crewDirs) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No crew directories found",
+		}
+	}
+
+	// Use first crew dir to check beads-sync
+	crewDir := crewDirs[0]
+
+	// Check if beads-sync branch exists
+	cmd := exec.Command("git", "rev-parse", "--verify", "beads-sync")
+	cmd.Dir = crewDir
+	if err := cmd.Run(); err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No beads-sync branch (single-clone setup)",
+		}
+	}
+
+	// Get diff between main and beads-sync, excluding .beads/
+	cmd = exec.Command("git", "diff", "--name-only", "main..beads-sync", "--", ".", ":(exclude).beads")
+	cmd.Dir = crewDir
+	out, err := cmd.Output()
+	if err != nil {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusWarning,
+			Message: "Could not diff main..beads-sync",
+			Details: []string{err.Error()},
+		}
+	}
+
+	files := strings.TrimSpace(string(out))
+	if files == "" {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No orphaned code on beads-sync",
+		}
+	}
+
+	// Filter to code files only
+	var codeFiles []string
+	for _, f := range strings.Split(files, "\n") {
+		if f == "" {
+			continue
+		}
+		// Check if it's a code file
+		if strings.HasSuffix(f, ".go") || strings.HasSuffix(f, ".md") ||
+			strings.HasSuffix(f, ".yaml") || strings.HasSuffix(f, ".yml") ||
+			strings.HasSuffix(f, ".json") || strings.HasSuffix(f, ".tmpl") {
+			codeFiles = append(codeFiles, f)
+		}
+	}
+
+	if len(codeFiles) == 0 {
+		return &CheckResult{
+			Name:    c.Name(),
+			Status:  StatusOK,
+			Message: "No orphaned code on beads-sync (only non-code files differ)",
+		}
+	}
+
+	return &CheckResult{
+		Name:    c.Name(),
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("%d file(s) on beads-sync not in main", len(codeFiles)),
+		Details: codeFiles,
+		FixHint: "Review with: git diff main..beads-sync -- <file>",
+	}
+}
+
+// findCrewDirs returns crew directories that might have beads-sync.
+func (c *BeadsSyncOrphanCheck) findCrewDirs(townRoot string) []string {
+	var dirs []string
+
+	entries, err := os.ReadDir(townRoot)
+	if err != nil {
+		return dirs
+	}
+
+	for _, entry := range entries {
+		if !entry.IsDir() || strings.HasPrefix(entry.Name(), ".") || entry.Name() == "mayor" {
+			continue
+		}
+
+		crewPath := filepath.Join(townRoot, entry.Name(), "crew")
+		if crewEntries, err := os.ReadDir(crewPath); err == nil {
+			for _, crew := range crewEntries {
+				if crew.IsDir() && !strings.HasPrefix(crew.Name(), ".") {
+					dirs = append(dirs, filepath.Join(crewPath, crew.Name()))
+				}
+			}
+		}
+	}
+
+	return dirs
+}