diff --git a/src/internationalization/ArcanistUSEnglishTranslation.php b/src/internationalization/ArcanistUSEnglishTranslation.php
--- a/src/internationalization/ArcanistUSEnglishTranslation.php
+++ b/src/internationalization/ArcanistUSEnglishTranslation.php
@@ -68,6 +68,16 @@
         'Ignore this untracked file and continue?',
         'Ignore these untracked files and continue?',
       ),
+
+      '%s submodule(s) have uncommitted or untracked changes:' => array(
+        'A submodule has uncommitted or untracked changes:',
+        'Submodules have uncommitted or untracked changes:',
+      ),
+
+      'Ignore the changes to these %s submodule(s) and continue?' => array(
+        'Ignore the change to this submodule and continue?',
+        'Ignore the changes to these submodules and continue?',
+      ),
     );
   }
 
diff --git a/src/repository/api/ArcanistGitAPI.php b/src/repository/api/ArcanistGitAPI.php
--- a/src/repository/api/ArcanistGitAPI.php
+++ b/src/repository/api/ArcanistGitAPI.php
@@ -672,7 +672,7 @@
     $result = new PhutilArrayWithDefaultValue();
 
     list($stdout) = $uncommitted_future->resolvex();
-    $uncommitted_files = $this->parseGitStatus($stdout);
+    $uncommitted_files = $this->parseGitRawDiff($stdout);
     foreach ($uncommitted_files as $path => $mask) {
       $result[$path] |= ($mask | self::FLAG_UNCOMMITTED);
     }
@@ -704,7 +704,7 @@
       $this->getDiffBaseOptions(),
       $this->getBaseCommit());
 
-    return $this->parseGitStatus($stdout);
+    return $this->parseGitRawDiff($stdout);
   }
 
   public function getGitConfig($key, $default = null) {
@@ -759,7 +759,7 @@
     return $this;
   }
 
-  private function parseGitStatus($status, $full = false) {
+  private function parseGitRawDiff($status, $full = false) {
     static $flags = array(
       'A' => self::FLAG_ADDED,
       'M' => self::FLAG_MODIFIED,
@@ -777,17 +777,51 @@
     $files = array();
     foreach ($lines as $line) {
       $mask = 0;
+
+      // "git diff --raw" lines begin with a ":" character.
+      $old_mode = ltrim($line[0], ':');
+      $new_mode = $line[1];
+
+      // The hashes may be padded with "." characters for alignment. Discard
+      // them.
+      $old_hash = rtrim($line[2], '.');
+      $new_hash = rtrim($line[3], '.');
+
       $flag = $line[4];
       $file = $line[5];
-      foreach ($flags as $key => $bits) {
-        if ($flag == $key) {
-          $mask |= $bits;
-        }
+
+      $new_value = intval($new_mode, 8);
+      $is_submodule = (($new_value & 0160000) === 0160000);
+
+      if (($is_submodule) &&
+          ($flag == 'M') &&
+          ($old_hash === $new_hash) &&
+          ($old_mode === $new_mode)) {
+        // See T9455. We see this submodule as "modified", but the old and new
+        // hashes are the same and the old and new modes are the same, so we
+        // don't directly see a modification.
+
+        // We can end up here if we have a submodule which has uncommitted
+        // changes inside of it (for example, the user has added untracked
+        // files or made uncommitted changes to files in the submodule). In
+        // this case, we set a different flag because we can't meaningfully
+        // give users the same prompt.
+
+        // Note that if the submodule has real changes from the parent
+        // perspective (the base commit has changed) and also has uncommitted
+        // changes, we'll only see the real changes and miss the uncommitted
+        // changes. At the time of writing, there is no reasonable porcelain
+        // for finding those changes, and the impact of this error seems small.
+
+        $mask |= self::FLAG_EXTERNALS;
+      } else if (isset($flags[$flag])) {
+        $mask |= $flags[$flag];
       }
+
       if ($full) {
         $files[$file] = array(
           'mask' => $mask,
-          'ref'  => rtrim($line[3], '.'),
+          'ref'  => $new_hash,
         );
       } else {
         $files[$file] = $mask;
@@ -807,7 +841,7 @@
     list($stdout) = $this->execxLocal(
       'diff --raw %s',
       $since_commit);
-    return $this->parseGitStatus($stdout);
+    return $this->parseGitRawDiff($stdout);
   }
 
   public function getBlame($path) {
diff --git a/src/repository/api/ArcanistRepositoryAPI.php b/src/repository/api/ArcanistRepositoryAPI.php
--- a/src/repository/api/ArcanistRepositoryAPI.php
+++ b/src/repository/api/ArcanistRepositoryAPI.php
@@ -15,6 +15,9 @@
   const FLAG_MISSING      = 32;
   const FLAG_UNSTAGED     = 64;
   const FLAG_UNCOMMITTED  = 128;
+
+  // Occurs in SVN when you have uncommitted changes to a modified external,
+  // or in Git when you have uncommitted or untracked changes in a submodule.
   const FLAG_EXTERNALS    = 256;
 
   // Occurs in SVN when you replace a file with a directory without telling
@@ -195,6 +198,14 @@
   /**
    * @task status
    */
+  final public function getDirtyExternalChanges() {
+    return $this->getUncommittedPathsWithMask(self::FLAG_EXTERNALS);
+  }
+
+
+  /**
+   * @task status
+   */
   private function getUncommittedPathsWithMask($mask) {
     $match = array();
     foreach ($this->getUncommittedStatus() as $path => $flags) {
diff --git a/src/workflow/ArcanistWorkflow.php b/src/workflow/ArcanistWorkflow.php
--- a/src/workflow/ArcanistWorkflow.php
+++ b/src/workflow/ArcanistWorkflow.php
@@ -893,11 +893,47 @@
           implode("\n    ", $missing)));
     }
 
+    $externals = $api->getDirtyExternalChanges();
+
+    // TODO: This state can exist in Subversion, but it is currently handled
+    // elsewhere. It should probably be handled here, eventually.
+    if ($api instanceof ArcanistSubversionAPI) {
+      $externals = array();
+    }
+
+    if ($externals) {
+      $message = pht(
+        '%s submodule(s) have uncommitted or untracked changes:',
+        new PhutilNumber(count($externals)));
+
+      $prompt = pht(
+        'Ignore the changes to these %s submodule(s) and continue?',
+        new PhutilNumber(count($externals)));
+
+      $list = id(new PhutilConsoleList())
+        ->setWrap(false)
+        ->addItems($externals);
+
+      id(new PhutilConsoleBlock())
+        ->addParagraph($message)
+        ->addList($list)
+        ->draw();
+
+      $ok = phutil_console_confirm($prompt, $default_no = false);
+      if (!$ok) {
+        throw new ArcanistUserAbortException();
+      }
+    }
+
     $uncommitted = $api->getUncommittedChanges();
     $unstaged = $api->getUnstagedChanges();
 
+    // We already dealt with externals.
+    $unstaged = array_diff($unstaged, $externals);
+
     // We only want files which are purely uncommitted.
     $uncommitted = array_diff($uncommitted, $unstaged);
+    $uncommitted = array_diff($uncommitted, $externals);
 
     $untracked = $api->getUntrackedChanges();
     if (!$this->shouldRequireCleanUntrackedFiles()) {