[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.

The AMPLab webserver that is used in the test occasionally hangs?  If so, we catch
the HttpHostConnectException that the Apache lib throws, wait five seconds, and try
once more.
Merge pull request #328 from genomebridge/adam-326

[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.
[ADAM-294] Replacing shade plugin with appassembler.
[ADAM-316] Adding native Java language bindings for ADAM.
Reformatting pom's to match Maven's 2 space indent convention (see http://maven.apache.org/developers/conventions/code.html)
[ADAM-318] Added code coverage capture via scoverage.
add count of mismatches to mdtag
Merge pull request #329 from hammerlab/mdtag-counts

Add count of mismatches to mdtag
[ADAM-331] Moving code coverage analysis into a profile, so it is not packaged into artifacts.
Merge pull request #334 from fnothaft/fix-ccov

Moving code coverage into a profile