Presubmit should be able to handle files being deleted.

tools/presubmit.py

 #!/usr/bin/env python
 #
 # Copyright 2012 the V8 project authors. All rights reserved.
 # Redistribution and use in source and binary forms, with or without
 # modification, are permitted provided that the following conditions are
 # met:
 #
 #     * Redistributions of source code must retain the above copyright
 #       notice, this list of conditions and the following disclaimer.
 #     * Redistributions in binary form must reproduce the above
@@ skipping 161 matching lines @@
     # Helper for getting directory pieces.
     dirs = lambda f: dirname(f).split(os.sep)
 
     # Path offsets where to look (to be in sync with RunOnPath).
     # Normalize '.' to check for it with str.startswith.
     search_paths = [('' if p == '.' else p) for p in self.GetPathsToSearch()]
 
     all_files = [
       f.AbsoluteLocalPath()
       for f in files
-      if (not self.IgnoreFile(f.LocalPath()) and
+      if (os.path.isfile(f.AbsoluteLocalPath()) and
+          not self.IgnoreFile(f.LocalPath()) and
           self.IsRelevant(f.LocalPath()) and
           all(not self.IgnoreDir(d) for d in dirs(f.LocalPath())) and
           any(map(f.LocalPath().startswith, search_paths)))
     ]
 
     return self.ProcessFiles(all_files)
 
   def IgnoreDir(self, name):
     return (name.startswith('.') or
             name in ('buildtools', 'data', 'gmock', 'gtest', 'kraken',
@@ skipping 328 matching lines @@
   success &= SourceProcessor().RunOnPath(workspace)
   success &= CheckStatusFiles(workspace)
   if success:
     return 0
   else:
     return 1
 
 
 if __name__ == '__main__':
   sys.exit(Main())