ci_runner: cleanup previously setup repo

Clean up well known files that could cause subsequent git operations to
fail.

enterprise/server/cmd/ci_runner/main.go

@@ -1633,6 +1633,9 @@ func (ws *workspace) setup(ctx context.Context) error {
 		if err := os.Chdir(repoDirName); err != nil {
 			return status.WrapError(err, "cd")
 		}
+		if err := ws.cleanup(ctx); err != nil {
+			return err
+		}
 		err := ws.sync(ctx)
 		if err == nil {
 			return nil
@@ -1690,6 +1693,27 @@ func (ws *workspace) applyPatch(ctx context.Context, bsClient bspb.ByteStreamCli
 	return nil
 }
 
+var gitTroubles = []string{
+	"index.lock",
+	"shallow.lock",
+	"HEAD.lock",
+	"hooks/post-checkout",
+	"config.lock",
+}
+
+func (ws *workspace) cleanup(ctx context.Context) error {
+	for _, f := range gitTroubles {
+		if err := os.Remove(filepath.Join(".git", f)); err != nil {
+			if strings.Contains(err.Error(), "no such file or directory") {
+				// It's good that the file does not exist
+				continue
+			}
+			return fmt.Errorf("failed to cleanup %s: %v", f, err)
+		}
+	}
+	return nil
+}
+
 func (ws *workspace) sync(ctx context.Context) error {
 	if *pushedBranch == "" && *commitSHA == "" {
 		return status.InvalidArgumentError("expected at least one of `pushed_branch` or `commit_sha` to be set")