Beginning refactoring for new CLI.
Disabled some tests that require OpenEye tools to allow travis-ci to be useful.
Draft command line skeleton.
'yank selftest' now tests all docstrings.
Added cli dispatch.
Drafted run command.
Added implementation of citations.
Drafted implementation of cleanup.
Implemented draft of status.
Draft of yank setup.
Ongoing major restructuring.  (Things are not working right now)
Checking in another batch of work (still broken!).
Update on current progress, which includes building in draft systembuilder functionality.
Holy crap, it may almost be working...
Minor bugfixes.  Still not fully working, since the resume() and create() schemes need to be updated.
Fixed some minor bugs with amber setup.
Added option to allow user to specify whether initial structures should be minimized.
Updated benzene-toluene example.
Renamed oldrepex -> repex, and minor bugfixes.
Fixed oldrepex -> repex imports, but now have to migrate testsystems into separate repo.