Fixed some issues with systembuilder and tests.
Several more systembuilder bugfixes.
Many more fixes to systembuilder.
Eliminated more bugs in systembuilder.
Fixed further issues with systembuilder.  May be running into gaff2xml limitations now.
Testing systembuilder in vacuum now.
Added workaround fix to ensure duplicate parameter files aren't included, but still not sure why duplicate parameter files were being included in the first place.
Still using vacuum by default instead of OBC GBSA.
Disabled PME testing.
Updated tests.
Squished more bugs.  Systembuilder doctests pass!
Merge pull request #78 from jchodera/master

Debugged systembuilder.