Remove dihedralindices command

This functionality is built in to the Dihedral
Featurizer
Remove fit[g,vm]hmm commands

These should use the generic fit command base class
Remove "unpack" command (just an empty file)
Remove commands for pulling structures

This sort of thing depends on how we implement data
saving / loading
Mixins is now unnecessary
Merge pull request #286 from mpharrigan/prune_old_commands

Prune old commands
Fix doc building