Regenerate all bnd_topo files in namelist_defaults using latest and greatest topo mods

[adamrher]

By "latest and greatest" I mean:

(1) new GMTED2010/BedMachine merged source topo: https://github.com/NCAR/Topo/issues/10 (2) bug fixes to Julio's ridge finding algorithm (no issue on NCAR/Topo yet) (3) Use new workflow to streamline the process (being developed on branch: https://github.com/NCAR/Topo/tree/topowopts)

While we are doing this, we should also cleanup the inputdata repo of topo files to remove any uncessary topo files, and make a more consistent directory structure (different directories for difference dycores?).

This will only be done for the SE and MPAS dycores.