Submit.csh: Resolve symlinks to f90 files when copying code

 - Copy also the .[fF]90 files that are just symbolic links to the MESHER directory (background_models.f90, clocks.f90...)
 - Copy also the .c files
submit.csh: Copy inparam_mesh and make_axisem.macros

 - Save these files in the rundir as well for forensic purposes