gemini3d/gemini-matlab: new API requiring Gemini >= 0.6.0

Enacted new Gemini API for unambiguous directory input. Directories in config.nml may be either absolute paths, or relative to the top-level output directory specified at the command line. To avoid future problems, developers should avoid using absolute_path() except in top-level scripts as necessary.

Numerous additional checks were added and self-tests added. Due to bugs in GNU Octave, even in the latest 5.2.0 release, Octave is not capable of writing HDF5 or NetCDF4 files. We have left full capability for Octave throughout this repo, in the hopes that the NetCDF4 bugs will be fixed.

added several utility functions of general use under matlab/fileio/ and matlab/sys/ for working with HDF5 and NetCDF4 files, as well as computing number of MPI images

added ability to run_gemini() from Matlab, just like Python gemini_run.

added ability to generate simulations iteratively over a directory