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
So mayby pmd/checkstyle/findbugs should filter only .java files in the same way?

Or its better to give option with files to filter?