fix issue with converting a folder on linux #683
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On linux since paths are case-sensitive, the code to automatically determine the files in a folder recursively fails.
I have fixed this by iterating over the folder and then applying custom logic to get the files.
This however brought around a change because the original functions to filter the files did not work in a case-sensitive way, so I changed the code to simply loop over all the files once and then pattern match them. Despite now using regex, this should still be the same if not faster than before since we now only need to loop over all the file sin the directory once.