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make directory layout more intelligible

David E. DeMarle requested to merge improve_file_layout into master

@tjcorona @alvaro.sanchez

With this we get a sane layout for the directory structure. Grab the pvsm file from testcase2 and play it in paraview. Then, put this code into place and play it again and then compare the file layouts.

As long as the viewer has this too, then both sides work fine.

Question: is this the most efficient way?

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