Simplify architecture selection, fix bug in file naming #33
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Now switching between gfortran and mpi requires only a single-line change in Makefile instead of needing to edit cms.f90.
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This PR does the following:
Ideally this PR would be split up and reorganized, but that would take time I would rather not devote to it, given that I think all parts of the PR should be merged.
The memory-overwrite bug in mod_directory.c was sometimes preventing the output files from being moved between "SCRATCH" and "output".
Some of the commits look more extensive than they actually are because I use an editor that strips trailing whitespace. Ideally, all trailing whitespace would already have been stripped.