diff --git a/src/configuration/ArcanistConfigurationManager.php b/src/configuration/ArcanistConfigurationManager.php
--- a/src/configuration/ArcanistConfigurationManager.php
+++ b/src/configuration/ArcanistConfigurationManager.php
@@ -100,7 +100,17 @@
     }
 
     $user_config = $this->readUserArcConfig();
-    $pval = idx($user_config, $key);
+
+    // For "aliases" coming from the user config file specifically, read the
+    // top level "aliases" key instead of the "aliases" key inside the "config"
+    // setting. Aliases were originally user-specific but later became standard
+    // configuration, which is why this works oddly.
+    if ($key === 'aliases') {
+      $pval = idx($this->readUserConfigurationFile(), $key);
+    } else {
+      $pval = idx($user_config, $key);
+    }
+
     if ($pval !== null) {
       $results[self::CONFIG_SOURCE_USER] =
         $settings->willReadValue($key, $pval);
diff --git a/src/workflow/ArcanistAliasWorkflow.php b/src/workflow/ArcanistAliasWorkflow.php
--- a/src/workflow/ArcanistAliasWorkflow.php
+++ b/src/workflow/ArcanistAliasWorkflow.php
@@ -59,17 +59,14 @@
 
   public static function getAliases(
     ArcanistConfigurationManager $configuration_manager) {
+    $sources = $configuration_manager->getConfigFromAllSources('aliases');
 
-    $working_copy_config_aliases =
-      $configuration_manager->getProjectConfig('aliases');
-    if (!$working_copy_config_aliases) {
-      $working_copy_config_aliases = array();
+    $aliases = array();
+    foreach ($sources as $source) {
+      $aliases += $source;
     }
-    $user_config_aliases = idx(
-      $configuration_manager->readUserConfigurationFile(),
-      'aliases',
-      array());
-    return $user_config_aliases + $working_copy_config_aliases;
+
+    return $aliases;
   }
 
   private function writeAliases(array $aliases) {