Updated class browser cache.
Updated `genome` tab completion.
CHANGELOG: Fix for the Candidate March 2013 Reference Alignment processing profile.
The FalsePositiveVcf filter will now function properly in the reference alignment pipeline as written by this processing profile.

Filter:
Do not remove existing vcfs if it is a file and not a symlink.

FalsePositiveVcf and VarFilterSnv:
Refactor out get_samples_from_header for code re-use. Now function either on snvs.hq (in vcf format) or snvs.vcf.gz to play nicely with refalign and PC respectively.
Still pretty hacky.

FalsePositiveVcf VarFilterSnv Filter:
added _check_native_file_counts_vcf to the Filter.pm base class for validating output that involves vcf headers.
updated jenkins submodule to e7c9b43
bug where tumor/normal segments didn't get input
updated sciclone to use github
moved Sciclone to the top level of gmt
moved CopyCat to a top-level namespace
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
GM: update output for import metadata
GM: import/export metadata uses utility test compare_ok
PerLaneTophat will now use 12 threads
skip ./. as .
fix warning message
added --canonical option to flag transcripts
Updated class browser cache.
Updated `genome` tab completion.
added display names to SR inputs and params