Small bundle of changes

- Changes in config file reading method (old was not working for me at all)
- Removed file filtering for stash (filtering should be done globally)
- Fixed PMD
- Added jacoco + coveralls (badge needs to be changed to right one after pull)
- Few other small fixes
Its Stash fasade..

In our environment we dont have much scala files.. and witch that filtreing stash was able to only analyze scala files.

That part should be put in Engine.java together with config option for it..