Added test of SystemBuilder-derived systems to alchemy nosetest.
Partway through refactoring SystemBuilder and cleaning up documentation.
Many refinements to the original SystemBuilder concept, simplifying things greatly.
Not yet to a fully working version, but closer.
Major overhaul to small molecule SystemBuilder and friends, borrowing from mmtools and Bas's improvements on them.
Still not quite ready yet, but getting there!
Updated .travis.yml to use openmm-dev and repex-dev.
Updated .travis.yml to use pymbar-dev
Fixed .travis.yml, which had gotten out of sync with main branch.
Merge remote-tracking branch 'upstream/master' into fix-alchemy

Conflicts:
	.travis.yml
Updated requirements to use openmm-dev and pymbar-dev conda packages.
Updated requirements or conda packaging.
Added nosetests back to travis-ci.
Checking in to finish debugging on cluster.
Added verbose output to nosetests so that travis-ci will not stall.
Minor fix to formal charge specification.
Merge pull request #62 from jchodera/fix-alchemy

Modifications to fix SystemBuilder -> AbsoluteAlchemicalFactor interactions (still more fixed that are needed)