Fixed error in phase names in `yank setup amber`.
Added unit test for 'setup binding amber', which is catching some other issues.
Fixed a potential issue with quote-encased unit-bearing quantities on the command line.
Renamed repex 'protocol' to 'options' to avoid confusion.
Fixed error in specifying number of iterations.
Renamed benzene-toluene examples to fit new naming scheme.
Added setup tests for explicit and implicit solvent, but still very slow because energies must be computed at setup.
Creation of NetCDF files now elides minimization and energy computation, but have not tested running from these files yet.
Fixed issues with saving/resuming options.
Updated a number of examples to new naming convention
travis script update for tests
Merge pull request #125 from jchodera/fix-phases

Fixed error in phase names in `yank setup amber`