Improvements to Structure alignment CLIs

This improves the CLIs for structure alignment methods (CeMain, FatCat*, SmithWaterman3d, etc.). The GUI parameters (configured through a ConfigStrucAligParams subclass) are now available through the command line as well. Enums are also allowed as parameters.

The wrapper scripts in protein-comparison-tool were updated. The version numbers of CE*, FATCAT*, and SmithWaterman3Daligner were incremented to reflect the changes.

Other AbstractUserArgumentParser subclasses downstream of BioJava will need to be updated to work with the new system.


This pull request supersedes #211.