diff --git a/src/applications/diffusion/conduit/DiffusionBranchQueryConduitAPIMethod.php b/src/applications/diffusion/conduit/DiffusionBranchQueryConduitAPIMethod.php
--- a/src/applications/diffusion/conduit/DiffusionBranchQueryConduitAPIMethod.php
+++ b/src/applications/diffusion/conduit/DiffusionBranchQueryConduitAPIMethod.php
@@ -46,22 +46,12 @@
 
       // NOTE: We can't use DiffusionLowLevelGitRefQuery here because
       // `git for-each-ref` does not support `--contains`.
-      if ($repository->isWorkingCopyBare()) {
-        list($stdout) = $repository->execxLocalCommand(
-          'branch --verbose --no-abbrev --contains %s -- %Ls',
-          $contains,
-          $patterns_argv);
-        $ref_map = DiffusionGitBranch::parseLocalBranchOutput(
-          $stdout);
-      } else {
-        list($stdout) = $repository->execxLocalCommand(
-          'branch -r --verbose --no-abbrev --contains %s -- %Ls',
-          $contains,
-          $patterns_argv);
-        $ref_map = DiffusionGitBranch::parseRemoteBranchOutput(
-          $stdout,
-          DiffusionGitBranch::DEFAULT_GIT_REMOTE);
-      }
+      list($stdout) = $repository->execxLocalCommand(
+        'branch --verbose --no-abbrev --contains %s -- %Ls',
+        $contains,
+        $patterns_argv);
+      $ref_map = DiffusionGitBranch::parseLocalBranchOutput(
+        $stdout);
 
       $refs = array();
       foreach ($ref_map as $ref => $commit) {
diff --git a/src/applications/diffusion/query/lowlevel/DiffusionLowLevelGitRefQuery.php b/src/applications/diffusion/query/lowlevel/DiffusionLowLevelGitRefQuery.php
--- a/src/applications/diffusion/query/lowlevel/DiffusionLowLevelGitRefQuery.php
+++ b/src/applications/diffusion/query/lowlevel/DiffusionLowLevelGitRefQuery.php
@@ -33,16 +33,9 @@
 
     $prefixes = array();
 
-    if ($repository->isWorkingCopyBare()) {
-      $branch_prefix = 'refs/heads/';
-    } else {
-      $remote = DiffusionGitBranch::DEFAULT_GIT_REMOTE;
-      $branch_prefix = 'refs/remotes/'.$remote.'/';
-    }
-
+    $branch_prefix = 'refs/heads/';
     $tag_prefix = 'refs/tags/';
 
-
     if ($with_refs || count($ref_types) > 1) {
       // If we're loading refs or more than one type of ref, just query
       // everything.
diff --git a/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php b/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
--- a/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
+++ b/src/applications/repository/engine/PhabricatorRepositoryPullEngine.php
@@ -366,8 +366,12 @@
 
     $fetch_rules = $this->getGitFetchRules($repository);
 
+    // For very old non-bare working copies, we need to use "--update-head-ok"
+    // to tell Git that it is allowed to overwrite whatever is currently
+    // checked out. See T13280.
+
     $future = $repository->getRemoteCommandFuture(
-      'fetch --prune -- %P %Ls',
+      'fetch --prune --update-head-ok -- %P %Ls',
       $repository->getRemoteURIEnvelope(),
       $fetch_rules);