Skip deleted files from symlink check

pkg/bootstrap/git/gogit/gogit.go

@@ -172,7 +172,13 @@ func (g *GoGit) Commit(message git.Commit, opts ...git.Option) (string, error) {
 	// modified. There's no circumstance in which we want to commit a
 	// change to a broken symlink: so, detect and skip those.
 	var changed bool
-	for file, _ := range status {
+	for file, fileStatus := range status {
+    if fileStatus.Staging == gogit.Deleted {
+      _, _ = wt.Add(file)
+      changed = true
+      continue
+    }
+
 		abspath := filepath.Join(g.path, file)
 		info, err := os.Lstat(abspath)
 		if err != nil {