Delete intermediate outputs even when they exist

Previously, cwltool would not delete intermediate output directories if
they contained any files, which rather negated the point of deleting
them. This behaviour goes back to at least cwltool version
1.0.20170723124118.

Author: keysmashes

cwltool/process.py

@@ -377,7 +377,7 @@ def relink(relinked,  # type: Dict[Text, Text]
 
 def cleanIntermediate(output_dirs):  # type: (Set[Text]) -> None
     for a in output_dirs:
-        if os.path.exists(a) and empty_subtree(a):
+        if os.path.exists(a):
             _logger.debug(u"Removing intermediate output directory %s", a)
             shutil.rmtree(a, True)