The issue is here: https://opensource.ncsa.illinois.edu/bitbucket/projects/WOLF/repos/datawolf/browse/datawolf-executor-commandline/src/main/java/edu/illinois/ncsa/datawolf/executor/commandline/CommandLineExecutor.java#164
One possible solution is to iterate over the file descriptor list and assuming the files in the list have unique names, possibly with file extensions, we can:
1) Check if each file has an extension and write the file to the run folder as "filename" + extension where filename comes from line 146. A user that specified "input" in the filename field when creating the tool, we would write, for example: input.shp, input.dbf and "input".
I'm open to other possible solutions to fix this issue.