If my program creates a subdirectory, when Pegasus cleans up it will remove the files but not the empty directories.

This makes it confusing, because after I run I can still have many empty subdirectories, even though there are no temporary files left for the run. So after a run, I have to look more closely through each directory to make sure everything did indeed succeed and that all directories are empty.

It would be nice if Pegasus did analysis to find all empty subdirectories (i.e. all dir/files have been deleted), and clean them up as it goes along if they are indeed empty. This way, after a run the temp space should be empty and on one glance I can tell if anything went wrong based on if there are directories or files that have no been cleaned up. I can also do a rmdir of the empty run00xx, without having to traverse the directory removing it's empty subdirectories (rm -Rf is scary here, in case there was a problem and a file is left uncleaned).