Refactoring

[mephenor]

Mostly refactoring in preparation of introducing unit tests for all important components of ModelPolisher. Two bugfixes are incorporated, however:

• Logic for using AnnotateDB was inverted and should be corrected now (missed this one in the code review)
• Version number in README is now changed to the correct one when running gradle, i.e. it should now be propagated to all appropriate places

Jackson dependency will be upgraded to newest version with the registry parser.