Remove output files that are empty after the patches have been applied. Normally this option is unnecessary, since patch can examine the time stamps on the header to determine whether a file should exist after patching. However, if the input is not a context diff or if patch is conforming to POSIX, patch does not remove empty patched files unless this option is given

pisi/util.py

@@ -500,7 +500,7 @@ def do_patch(sourceDir, patchFile, level = 0):
         (ret, out, err) = run_batch('quilt push')
     else:
         # run GNU patch to apply original patch into tree
-        (ret, out, err) = run_batch("patch -p%d < \"%s\"" % (level, patchFile))
+        (ret, out, err) = run_batch("patch --remove-empty-files -p%d < \"%s\"" % (level, patchFile))
 
     if ret:
         if out is None and err is None: