Merge branch 'develop'
Refactored the compression interface per sample in ReduceReadsa

The CompressionStash is now responsible for keeping track of all intervals that must be kept uncompressed by all samples. In general this is a list generated by a tumor sample that will enforce all normal samples to abide.
  - Updated ReduceReads integration tests
  - Sliding Window is now using the CompressionStash (single sample).

DEV-104 #resolve #time 3m
Added another utility that can convert to RemoteFiles.
QScripts will now generate remote versions of files if the caller has not already passed in remote versions (or the QScript replaces the passed in remote references... not good)
Instead of having yet another plugin, combined QStatusMessenger and RemoteFileConverter under general QCommandPlugin trait.
Updated CMIBAMPP to use latest design of script() generating local paths and pushing bits back to <provided_s3_bucket/<provided_s3_prefix><argument fullName>.
Add uniform threading argument and enable multithreading in BQSR - will save over 40 hours of runtime
Fix merge conflicts
comment out QC metrics until picard jar path gets resolved
Revert "comment out QC metrics until picard jar path gets resolved"

This reverts commit 02049178662d1f7142e9df70502881264bd2ab81.
Undo git mess - revert back to origin and THEN comment out QC metrics
* resolved [DEV-88]
Intermediate fix
redo QC picard parts
a) Resolve [#DEV-56] - test data with indels in new directory private/testdata/CMITestData/. b) Skeleton (not yet working) of fastq-BAM unit test, c) misc bug fixes for QC functions to work (not done yet)
More test data for fastq-bam: new short.interval_list with correct header based on reference dict.
b) New interval/bait sets with corrected header for decoy contig in b37
c) New metadata file for test fastqs
d) Updated test fastqs as previous version was generated with bad intervals
Add support for calculating DoC with flanking intervals added
Adding integration test to ReduceReads coreduction
DEV-117 #resolve
Merge GATK repo into CMI-GATK

Bringing in the following relevant changes:
	* Fixes the indel realigner N-Way out null pointer exception DEV-10
	* Optimizations to ReduceReads that bring the run time to 1/3rd.

Conflicts:
	protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

DEV-10 #resolve #time 2m
Updating RR integration tests

Forgot to update the integration tests after merging DEV-117 with optimizations from GATK main repo.
When gathering VCFs, using CombineVariants from the current classpath, and not the GATK used to run the command. This was a concern for external modules that bundled the engine but not CombineVariants.
DEV-116 #resolve #time 3m