diff --git a/iq.drush.inc b/iq.drush.inc
index 3bb39683630e6f07ebbd5a3e2ea07dec0152d18e..4c7acbd24a3459b3bc0f4f16a0fbbcb149c4e39c 100644
--- a/iq.drush.inc
+++ b/iq.drush.inc
@@ -565,23 +565,23 @@ function drush_iq_apply_patch($number) {
       }
     }
     $result = drush_shell_exec_interactive('patch -Np%d --batch -d %s -i %s', $strip_count, $project_dir, $filename);
-    if (!drush_get_option('no-commit', FALSE)) {
-      $commit_comment = _drush_iq_create_commit_comment($issue_info, drush_get_option('committer', FALSE), drush_get_option('message', FALSE));
-      // TODO: can we easily ignore *.patch, etc., or easily add only modified files?
-      $result = drush_shell_exec("git add .");
-      if (dirname($filename) == $project_dir) {
-        $result = drush_shell_exec("git rm --cached -- %s", basename($filename));
-        if ($keep_patch) {
-          $result = drush_shell_exec("git rm --cached -- %s", basename($keep_patch));
-        }
-      }
-      if (array_key_exists('patchAuthorCredit', $issue_info)) {
-        $result = drush_shell_exec("git commit --author=%s -m %s", $issue_info['patchAuthorCredit'], $commit_comment);
-      }
-      else {
-        $result = drush_shell_exec("git commit -m %s", $commit_comment);
+  }
+  if (!drush_get_option('no-commit', FALSE)) {
+    $commit_comment = _drush_iq_create_commit_comment($issue_info, drush_get_option('committer', FALSE), drush_get_option('message', FALSE));
+    // Add the modified files
+    $result = drush_shell_exec("git add -A");
+    if (dirname($filename) == $project_dir) {
+      $result = drush_shell_exec("git rm --cached -- %s", basename($filename));
+      if ($keep_patch) {
+        $result = drush_shell_exec("git rm --cached -- %s", basename($keep_patch));
       }
     }
+    if (array_key_exists('patchAuthorCredit', $issue_info)) {
+      $result = drush_shell_exec("git commit --author=%s -m %s", $issue_info['patchAuthorCredit'], $commit_comment);
+    }
+    else {
+      $result = drush_shell_exec("git commit -m %s", $commit_comment);
+    }
   }
   drush_op('chdir', $cwd);
   return $issue_info;
@@ -913,11 +913,8 @@ function _drush_iq_project_dir(&$issue_info) {
         if (array_key_exists($project_name, $extension_info)) {
           $result = drush_get_context('DRUSH_DRUPAL_ROOT', '') . '/' . dirname($extension_info[$project_name]->filename);
         }
-        else {
-          drush_log(dt('Could not find the project directory under the bootstrapped site'));
-        }
       }
-      elseif ($phase >= DRUSH_BOOTSTRAP_DRUPAL_ROOT) {
+      if ($phase >= DRUSH_BOOTSTRAP_DRUPAL_ROOT) {
         $root = drush_get_context('DRUSH_DRUPAL_ROOT', FALSE);
         if ($root) {
           if ($project_name == 'drupal') {
@@ -937,6 +934,9 @@ function _drush_iq_project_dir(&$issue_info) {
     if ($result) {
       $issue_info['project-dir'] = $result;
     }
+    else {
+      drush_log(dt('Could not find the project directory under the bootstrapped site'));
+    }
   }
 
   return $result;