CheckStyles/code cleanup and JavaDoc

Last of the nearly-purely-cleanup PRs for a bit, I promise.  I hit all of this while wrapping my head around how to approach the test suite issue.  This does get us down to 479 CheckStyles violations, though, basically all of which are just CheckStyles whinging about the lack of JavaDoc on protected members, and eliminates a lot of stuff that was picked up by IntelliJ and findbugs on general code cleanliness.