Update refactor branch

LocusPocus on the "refactor" branch is the most stable and up-to-date version. The reason this has not been merged back into the main "master" branch is that the up-to-date version of ParsEval on this branch is not yet complete. I haven't had time to work on AEGeAn recently, but hope to take care of this soon.

In the mean time, everyone should at least have access to the latest version of LocusPocus.