Use biopet flagstat as fallback values in case Picard CollectAlignmentSummaryMetrics has incorrect output/

Apparently sbt-coveralls 1.0.x is only compatible with sbt-scoverage 1.0.x.
See: https://github.com/scoverage/sbt-coveralls/issues/49

Since it's already the same as what we are using (sbt-extras).
See: https://github.com/travis-ci/travis-ci/issues/3140

Also, replace git-stamp plugin with newer version since one of its
dependency is binary-incompatible with sbt-coveralls.

Thanks to input from Sander van der Zeeuw.