Code cleanup

[jeffreyguenther]

• [ ] Fix Port toCode() method to work with all port types
• [ ] Write method javadocs for all classes
• [ ] Organize SubjunctiveParametricSystem methods by use (Setup, search, etc)
• [ ] Fix Shiro.java so that it works from the commandline.
• [ ] Migrate code, where possible to java.nio.Path instead of File

[jeffreyguenther]

Old issue. Not relevant in current repo anymore. We have better code :smile: