diff --git a/fdroidserver/index.py b/fdroidserver/index.py
index d8477dc5..29027a38 100644
--- a/fdroidserver/index.py
+++ b/fdroidserver/index.py
@@ -88,7 +88,7 @@ def make(apps, sortedids, apks, repodir, archive):
 
     mirrorcheckfailed = False
     mirrors = []
-    for mirror in sorted(common.config.get('mirrors', [])):
+    for mirror in common.config.get('mirrors', []):
         base = os.path.basename(urllib.parse.urlparse(mirror).path.rstrip('/'))
         if common.config.get('nonstandardwebroot') is not True and base != 'fdroid':
             logging.error(_("mirror '%s' does not end with 'fdroid'!") % mirror)
diff --git a/fdroidserver/nightly.py b/fdroidserver/nightly.py
index 9579ae50..e6f766c0 100644
--- a/fdroidserver/nightly.py
+++ b/fdroidserver/nightly.py
@@ -249,8 +249,8 @@ Last updated: {date}'''.format(repo_git_base=repo_git_base,
         common.assert_config_keystore(config)
 
         for root, dirs, files in os.walk(cibase):
-            for d in ('fdroid', '.git', '.gradle'):
-                if d in dirs:
+            for d in dirs:
+                if d == '.git' or d == '.gradle' or (d == 'fdroid' and root == cibase):
                     dirs.remove(d)
             for f in files:
                 if f.endswith('-debug.apk'):