Porting all PyCogent's app controllers to brokit

Completely removes the dependencies on PyCogent's app controllers an rely on the brokit app controllers.

Specifically, the app controllers moved are:

- infernal
- clustalw
- muscle_v38
- formatdb
- blast
- raxml_v730
- fasttree
- clearcut
- rdp
- parsinsert
- cdhit
- mothur
- pplacer
- rtax