Don't fall over if run with no arguments.
Fix paths to dependent DLLs.
Switch from SVN to git.
Update instructions on building the documentation.
Document the .refined files.
Remove unused ConfigurationSet.
Fix unused object warnings.
Don't try to calculate distance/angle statistics if we don't have a reference
structure.
Show the final model.
Don't import numpy unless we really need it.
Ignore vim swap files.
Demonstrate MultiFit clustering.
Don't try to set transformation if there is no reference PDB.
Fix unused object warnings.
Remove multi-processor option, since it doesn't work.
Make refine_fft command available and test it.
Demonstrate and test MultiFit refinement.
Remove obsolete examples.
Fix typo.
Fix typo.