Make sure to handle deleted prefixes properly

util/streamlayerformat.py

@@ -89,9 +89,14 @@ class StreamLayerMerger(object):
     # Check if this file has already been encountered somewhere. If so,
     # skip it.
     ubsolute = unicode(absolute)
-    if ubsolute in self.path_trie or any(self.prefix_trie.iter_prefixes(ubsolute)):
+    if ubsolute in self.path_trie:
       return False
 
+    # Check if this file is under a deleted path.
+    for prefix in self.prefix_trie.iter_prefixes(ubsolute):
+      if not os.path.relpath(ubsolute, prefix).startswith('..'):
+        return False
+
     # Otherwise, add the path to the encountered list and return it.
     self.path_encountered.append(absolute)
     return True