Adding motif incorporation and bigfix for LoopMover_Backrub.
1. New application for incorporating motifs into flexible loops.
2. Fixed bug in LoopMover_Backrub that prevented proper use of stored scorefunctions that were provided to the constructor.
3. Saw integration test changes in:
match_1n91
inverse_rotamer_remodel
match_6cpa
cstfile_to_theozyme_pdb