diff --git a/main.go b/main.go
index 8c6f48d..fa5e528 100644
--- a/main.go
+++ b/main.go
@@ -188,15 +188,7 @@ func applyCmd(args []string) error {
 	}
 
 	fmt.Printf("Stale links found: %d\n", len(stales))
-	ok, err := promptYesNo("Prune them?", false)
-	if err != nil {
-		return err
-	}
-	if ok {
-		return removeLinks(stales, false)
-	}
-
-	return nil
+	return handleStaleLinks(stales)
 }
 
 func addCmd(args []string) error {
@@ -761,6 +753,104 @@ func removeLinks(paths []string, dryRun bool) error {
 	return nil
 }
 
+func handleStaleLinks(stales []string) error {
+	if len(stales) == 0 {
+		return nil
+	}
+
+	repo, err := repoPath()
+	if err != nil {
+		return err
+	}
+
+	reader := bufio.NewReader(os.Stdin)
+	for _, path := range stales {
+		fmt.Printf("stale: %s\n", path)
+		fmt.Print("action [p=prune, u=unlink, i=ignore]: ")
+		choice, err := reader.ReadString('\n')
+		if err != nil {
+			return err
+		}
+		choice = strings.TrimSpace(strings.ToLower(choice))
+		if choice == "" || choice == "i" {
+			continue
+		}
+		if choice == "p" {
+			if err := os.Remove(path); err != nil {
+				return err
+			}
+			fmt.Printf("removed %s\n", path)
+			continue
+		}
+		if choice == "u" {
+			if err := unlinkStale(path, repo); err != nil {
+				return err
+			}
+			continue
+		}
+		fmt.Println("invalid choice; skipping")
+	}
+
+	return nil
+}
+
+func unlinkStale(targetPath, repo string) error {
+	info, err := os.Lstat(targetPath)
+	if err != nil {
+		return err
+	}
+	if info.Mode()&os.ModeSymlink == 0 {
+		return nil
+	}
+
+	src, err := os.Readlink(targetPath)
+	if err != nil {
+		return err
+	}
+	if !filepath.IsAbs(src) {
+		src = filepath.Join(filepath.Dir(targetPath), src)
+	}
+	src = filepath.Clean(src)
+
+	repoAbs, err := filepath.Abs(repo)
+	if err != nil {
+		return err
+	}
+
+	rel, err := filepath.Rel(repoAbs, src)
+	if err != nil {
+		return err
+	}
+	if strings.HasPrefix(rel, "..") {
+		return nil
+	}
+
+	parts := strings.Split(rel, string(os.PathSeparator))
+	if len(parts) < 3 {
+		return nil
+	}
+
+	if parts[1] != filesDirName {
+		return nil
+	}
+
+	repoPath := filepath.Join(repoAbs, rel)
+	if err := os.Remove(targetPath); err != nil {
+		return err
+	}
+
+	if err := copyFile(repoPath, targetPath); err != nil {
+		return err
+	}
+
+	if err := os.Remove(repoPath); err != nil {
+		return err
+	}
+
+	fmt.Printf("unlinked %s (removed %s)\n", targetPath, repoPath)
+	return nil
+}
+
 func restorePackage(filesDir, targetRoot string, dryRun bool) error {
 	filesAbs, err := filepath.Abs(filesDir)
 	if err != nil {