[#1662] Evolutions down from modules remove all others evolutions (modules, application)

Fix issues:
[#1662](http://play.lighthouseapp.com/projects/57987-play-framework/tickets/1662-evolutions-down-from-modules-remove-all-others-evolutions-modules-application)
[#1663] (http://play.lighthouseapp.com/projects/57987-play-framework/tickets/1663-when-starting-play-play-try-to-load-library-as-module)