Fix several regridding issues in file_regrid.py

gcpy_file_regrid.py
- Move flip_lev_coord_if_necessary so that it occurs before
  variable renaming/regridding.  This prevents the flipping algorithm
  from being spoofed by renamed variables.
- Renamed "drop_and_rename_classic_variables" to "drop_classic_vars",
  which only drops the non-regriddable variables.
- Move variable renaming into "rename_restart_variables".  Also improve
  logic so that variables are renamed properly
- Updated logic in the flip_lev_coord_if_necessary routine.  Also
  make sure to save coordinates in the proper order.  GCHP level
  coordinates are now saved as indices.
- Updated Pydoc and comments.
- Trimmed trailing whitespace.

gcpy/util.py
- Initialize "old_to_new" to a blank dictionary object

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>