diff --git a/internal/cmd/docs/cmd_sync.go b/internal/cmd/docs/cmd_sync.go
index 2cbfb4dc..a1611056 100644
--- a/internal/cmd/docs/cmd_sync.go
+++ b/internal/cmd/docs/cmd_sync.go
@@ -126,8 +126,8 @@ func runDocsSync(registryPath string, outputDir string, dryRun bool) error {
 		outName := packageOutputName(info.Name)
 		repoOutDir := filepath.Join(outputDir, outName)
 
-		// Clear existing directory
-		io.Local.Delete(repoOutDir) // Recursive delete
+		// Clear existing directory (recursively)
+		_ = io.Local.DeleteAll(repoOutDir)
 
 		if err := io.Local.EnsureDir(repoOutDir); err != nil {
 			cli.Print("  %s %s: %s\n", errorStyle.Render("✗"), info.Name, err)
diff --git a/internal/cmd/pkgcmd/cmd_install.go b/internal/cmd/pkgcmd/cmd_install.go
index d3d0bf55..b5052325 100644
--- a/internal/cmd/pkgcmd/cmd_install.go
+++ b/internal/cmd/pkgcmd/cmd_install.go
@@ -74,7 +74,7 @@ func runPkgInstall(repoArg, targetDir string, addToRegistry bool) error {
 
 	repoPath := filepath.Join(targetDir, repoName)
 
-	if _, err := coreio.Local.List(filepath.Join(repoPath, ".git")); err == nil {
+	if coreio.Local.Exists(filepath.Join(repoPath, ".git")) {
 		fmt.Printf("%s %s\n", dimStyle.Render(i18n.Label("skip")), i18n.T("cmd.pkg.install.already_exists", map[string]string{"Name": repoName, "Path": repoPath}))
 		return nil
 	}
diff --git a/internal/cmd/pkgcmd/cmd_manage.go b/internal/cmd/pkgcmd/cmd_manage.go
index cabba86f..cabcbde1 100644
--- a/internal/cmd/pkgcmd/cmd_manage.go
+++ b/internal/cmd/pkgcmd/cmd_manage.go
@@ -57,9 +57,8 @@ func runPkgList() error {
 	var installed, missing int
 	for _, r := range allRepos {
 		repoPath := filepath.Join(basePath, r.Name)
-		exists := false
-		if _, err := coreio.Local.List(filepath.Join(repoPath, ".git")); err == nil {
-			exists = true
+		exists := coreio.Local.Exists(filepath.Join(repoPath, ".git"))
+		if exists {
 			installed++
 		} else {
 			missing++
@@ -219,7 +218,7 @@ func runPkgOutdated() error {
 	for _, r := range reg.List() {
 		repoPath := filepath.Join(basePath, r.Name)
 
-		if _, err := coreio.Local.List(filepath.Join(repoPath, ".git")); err != nil {
+		if !coreio.Local.Exists(filepath.Join(repoPath, ".git")) {
 			notInstalled++
 			continue
 		}
diff --git a/internal/cmd/setup/cmd_bootstrap.go b/internal/cmd/setup/cmd_bootstrap.go
index a7d354ec..4ea2839c 100644
--- a/internal/cmd/setup/cmd_bootstrap.go
+++ b/internal/cmd/setup/cmd_bootstrap.go
@@ -105,7 +105,7 @@ func runBootstrap(ctx context.Context, only string, dryRun, all bool, projectNam
 
 	// Clone core-devops first
 	devopsPath := filepath.Join(targetDir, devopsRepo)
-	if _, err := coreio.Local.List(filepath.Join(devopsPath, ".git")); err != nil {
+	if !coreio.Local.Exists(filepath.Join(devopsPath, ".git")) {
 		fmt.Printf("%s %s %s...\n", dimStyle.Render(">>"), i18n.T("common.status.cloning"), devopsRepo)
 
 		if !dryRun {
@@ -148,9 +148,9 @@ func runBootstrap(ctx context.Context, only string, dryRun, all bool, projectNam
 }
 
 // isGitRepoRoot returns true if the directory is a git repository root.
+// Handles both regular repos (.git is a directory) and worktrees (.git is a file).
 func isGitRepoRoot(path string) bool {
-	_, err := coreio.Local.List(filepath.Join(path, ".git"))
-	return err == nil
+	return coreio.Local.Exists(filepath.Join(path, ".git"))
 }
 
 // isDirEmpty returns true if the directory is empty or contains only hidden files.
diff --git a/internal/cmd/setup/cmd_registry.go b/internal/cmd/setup/cmd_registry.go
index 896a4e63..d9714329 100644
--- a/internal/cmd/setup/cmd_registry.go
+++ b/internal/cmd/setup/cmd_registry.go
@@ -118,7 +118,7 @@ func runRegistrySetupWithReg(ctx context.Context, reg *repos.Registry, registryP
 			// Check if already exists
 			repoPath := filepath.Join(basePath, repo.Name)
 			// Check .git dir existence via List
-			if _, err := coreio.Local.List(filepath.Join(repoPath, ".git")); err == nil {
+			if coreio.Local.Exists(filepath.Join(repoPath, ".git")) {
 				exists++
 				continue
 			}
@@ -147,7 +147,7 @@ func runRegistrySetupWithReg(ctx context.Context, reg *repos.Registry, registryP
 
 			// Check if already exists
 			repoPath := filepath.Join(basePath, repo.Name)
-			if _, err := coreio.Local.List(filepath.Join(repoPath, ".git")); err == nil {
+			if coreio.Local.Exists(filepath.Join(repoPath, ".git")) {
 				exists++
 				continue
 			}
diff --git a/pkg/io/io.go b/pkg/io/io.go
index e542872c..1e5020b7 100644
--- a/pkg/io/io.go
+++ b/pkg/io/io.go
@@ -276,22 +276,32 @@ func (m *MockMedium) Rename(oldPath, newPath string) error {
 			newPrefix += "/"
 		}
 
-		// Move files under this directory
+		// Collect files to move first (don't mutate during iteration)
+		filesToMove := make(map[string]string)
 		for f, content := range m.Files {
 			if strings.HasPrefix(f, oldPrefix) {
 				newF := newPrefix + strings.TrimPrefix(f, oldPrefix)
-				m.Files[newF] = content
-				delete(m.Files, f)
+				filesToMove[f] = newF
+				_ = content // content will be copied in next loop
 			}
 		}
-		// Move subdirectories
+		for oldF, newF := range filesToMove {
+			m.Files[newF] = m.Files[oldF]
+			delete(m.Files, oldF)
+		}
+
+		// Collect directories to move first
+		dirsToMove := make(map[string]string)
 		for d := range m.Dirs {
 			if strings.HasPrefix(d, oldPrefix) {
 				newD := newPrefix + strings.TrimPrefix(d, oldPrefix)
-				m.Dirs[newD] = true
-				delete(m.Dirs, d)
+				dirsToMove[d] = newD
 			}
 		}
+		for oldD, newD := range dirsToMove {
+			m.Dirs[newD] = true
+			delete(m.Dirs, oldD)
+		}
 		return nil
 	}
 	return coreerr.E("io.MockMedium.Rename", "path not found: "+oldPath, os.ErrNotExist)