Handling duplicate remote filenames in WQ

This is very minor but it affects the user. Right now, we check for duplicate remote filesnames for both inputs and outputs in task_specify_file() and throw an error if so. 

This makes sense for input files when two different files are being mapped to the same remote filename. But this isn't the case for output files because a single remote file is being mapped to two different filenames.

In this fix, for outputs - we check for duplicate local filenames with different remote names. 
                    inputs -  we check for duplicate remote filenames with the different local filenames. 

@dthain, @btovar