-e option deletes all files in the specified folder
If you use java -jar PseuCoCo.jar -i <filepath> -e <folderpath>
and use as <folderpath>
a folder that contains files, all files are deleted. Subfolders are not affected.
I'm using an up-to-date Windows-10-PC with JDK-version 1.8.0_131.
As far as I can tell, you can reproduce this behaviour with any PseuCo-file and any folder.