Upgrade from Hadoop-BAM 5.3 to 6.0

This commit removes the checked in local maven repo and replaces
it with a remote private one. This helps to avoid checking large
files into this git repo.

In order to reduce dependencies, the BCF/VCF code has been removed
from Hadoop-BAM. I've talked with the Hadoop-BAM team about how
to publish maven artifacts that are compatible with all versions of
Hadoop. In the future, we will remove the Hadoop-BAM source
altogether and simply depend on a published artifact.
New AdamContext and RichAdamRecord decorators. New RDD methods. Schema fixes.

o Created a new AdamContext decorator for SparkContexts with methods for
  creating new ADAM RDDs from SAM/BAM or ADAM files
o New methods added to RDDs created by ADAM for aggregating pileups, sorting, and
  saving. Makes it easy to compose transformations, e.g. rdd.sort().markDups().save()
o Added new 'RichAdamRecord' decorator for ADAMRecords with useful utility methods
o Fixed a 1-off bug in mateReferencePosition. All offsets are now 0-based.
o Removed the 'end' field from an ADAMRecord and added 'mateReferenceId'
Fix case-sensitivity issue with last commit
Exclude the Eclipse Java development tools from shaded jar
Improve the performance of ReferencePosition.compare()