diff --git a/ops.go b/ops.go
index 8f232e6..e2d7606 100644
--- a/ops.go
+++ b/ops.go
@@ -93,8 +93,13 @@ func findStaleLinks(filesDir, targetRoot string) ([]string, error) {
 		return nil, err
 	}
 
+	targetAbs, err := filepath.Abs(targetRoot)
+	if err != nil {
+		return nil, err
+	}
+
 	var stale []string
-	walkErr := filepath.WalkDir(targetRoot, func(path string, entry fs.DirEntry, err error) error {
+	walkErr := filepath.WalkDir(filesDir, func(path string, entry fs.DirEntry, err error) error {
 		if err != nil {
 			return err
 		}
@@ -102,29 +107,43 @@ func findStaleLinks(filesDir, targetRoot string) ([]string, error) {
 			return nil
 		}
 
-		info, err := os.Lstat(path)
+		rel, err := filepath.Rel(filesAbs, path)
 		if err != nil {
 			return err
 		}
+
+		targetPath := filepath.Join(targetAbs, rel)
+		info, err := os.Lstat(targetPath)
+		if err != nil {
+			if errors.Is(err, os.ErrNotExist) {
+				// Symlink doesn't exist - not stale, just not applied
+				return nil
+			}
+			return err
+		}
+
 		if info.Mode()&os.ModeSymlink == 0 {
+			// Not a symlink, skip
 			return nil
 		}
 
-		src, err := os.Readlink(path)
+		src, err := os.Readlink(targetPath)
 		if err != nil {
 			return err
 		}
 		if !filepath.IsAbs(src) {
-			src = filepath.Join(filepath.Dir(path), src)
+			src = filepath.Join(filepath.Dir(targetPath), src)
 		}
 		src = filepath.Clean(src)
 
+		// Only consider symlinks pointing to our repo
 		if !strings.HasPrefix(src, filesAbs+string(os.PathSeparator)) && src != filesAbs {
 			return nil
 		}
 
+		// Check if the source file in repo still exists
 		if _, err := os.Stat(src); errors.Is(err, os.ErrNotExist) {
-			stale = append(stale, path)
+			stale = append(stale, targetPath)
 		}
 		return nil
 	})