Refactor

Create a SpecFiltering package and put SpecFilter and Configuraiton classes into that package, as we discussed yesterday.

Put several commonly used top-level classes into Util.

Inline FileConverter into JavaMOPOptions and lift it to top-level, since it is strongly correlated to JavaMOPMain

@kheradmand @xiaohe27 and @yzhang90 please review, before we proceed to further refactoring.