Simplify architecture selection, fix bug in file naming

[efiring]

This PR does the following:

• Adds a .gitignore file.
• Fixes a memory-overwriting bug in the file-renaming code.
• Adds a generic single-processor gfortran architecture.
• Localizes the selection of the architecture to a single line in Makefile, so nothing else needs to be edited.

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.