ClinSeq - various fixes related to work flow updated some, tests, etc.
Pass along the gap and centromere files we're making.
Fix cached version of help for phenotype-correlation
Remove GENOME_TEST_TEMP from more tests
Can now run Cufflinks w/ multiple modes in RnaSeq

It is now possible to specify a comma-separated list of values for
annotation_reference_transcripts_mode in RnaSeq processing profiles.
Updated tab completion for new additions to clinseq commands
updated ur submodule to 97317f1
removing default build
added is_last_complete to builds so groups of builds under model groups can be limited to just one per model