gemini3d/gemini: Add numerous checks, simplify CLI

gemini.bin command line now has only one mandatory argument: the top-level output directory. The inputs/config.nml should already be in there when gemini.bin is run. if the user doesn't specify an output file_format, Gemini.bin will use the same file format as the input/simsize.*. Check for NaNs and impossible values in several more places. correct potential source calculation error eliminate stack overflow in tests by using allocate() allow non-MPI unit tests to build even without MPI auto-download and auto-setup PyGemini if needed eliminate duplicative specification of "flags" in config.nml. Use presence of namelists to determine if an input is desired. allow namelists to be read in a different order than in file move all Python scripts to PyGemini except for bare minimum used for self-tests add optional EIA namelist make several .f90 files generated to cut down on linking for minimal parameters (faster parallel builds) add -dryrun to C