ShapeWorks should not require globally unique filenames

[akenmorris]

• https://shapeworks.discourse.group/t/trouble-getting-the-right-alignment-using-python/184/3

It appears that ShapeWorks requires filenames to be globally unique instead of allowing for different folders. This is probably due to the fact that the groomed and particle files get written to a single directory rather than a tree matching the input structure.