Interval List Tool:

added functionality so that tool can use a vcf as a source for intervals.
removing explain-flags.html from master as it now lives in the gh-pages branch
Merge pull request #131 from broadinstitute/nh_remove_explain_flags_from_master

removing explain-flags.html from master as it now lives in the gh-pages ...
fix build based on commit 59b1e89e182b56eb7ae44ac09259862c88dd2650
Merge pull request #132 from broadinstitute/nh_fix_build_xml

fix build based on commit 59b1e89e182b56eb7ae44ac09259862c88dd2650
Merge pull request #105 from broadinstitute/yf_merge_VCF_to_IntervalList_and_ILTOOLS

Interval List Tool:
allow colors to be disabled with -Dpicard.cmdline.color_status=false
adding the --list-commands argument to the main command line, to list
all the commands available without formatting.
Merge pull request #133 from broadinstitute/nh_issue_123

Nh issue 123
- Refactoring CollectWgsMetrics in order to be able to easily create
CollectRawWGSMetrics.
- Create RawWGSMetrics by overriding some default option values and
  repackaging the metrics class.
- Moved CollectIlluminaSummaryMetrics (will be deleted eventually)
- Fixed some test files.