CEMirrorSymm updates

* Mirror sequence, coordinates, or both.
* Searches for CPs by default
* Display rotation axes (not always meaningful)
CEsymmGUI. Reenable prompt.

This keeps getting accidentally commented out during testing.
Fix CeSymm distanceMatrix

Distance matrices were not being stored. Now
saved and properly post-processed.
CEMirrorSymm improvements

* Inherits from CESymm not CECP, to prevent trivial alignments
* Properly set the distance matrix for reversed alignments
Removing hard-coded path.

Douglas, add it to your VM arguments instead:
    -DPDB_DIR=/Users/dmyerstu/Desktop/the_pdb/
    -DPDB_CACHE_DIR=/Users/dmyerstu/Desktop/the_pdb/
SymmRefiner improvements

* Set a few more properties in the refined AFP
* Superficial changes to main method
Removing hard-coded PDB_DIR settings.

Add them to your default VM arguments instead, a la
    -DPDB_DIR=/tmp/pdb
    -DPDB_CACHE_DIR=/tmp/pdb
Merge branch 'master' of github.com:rcsb/symmetry