Revert "Merge branch 'allpaths' into gb_master"

This reverts commit 5edbb532a618d393014fc4ca120e3780b462b98a, reversing
changes made to 0b1e5c6e476a4f6f7c6b6fe994510af3bd492eb4.
updated workflow submodule to 810ef16
Refactor SxResult
New MergedSxResult
Merge branch 'allpaths' into gb_master
bug fix files md5 content info can be stored in aryref but it was coded to only look for it in hash structure
Added additional methods for fixing alpha (instead of numeric) GT values, such as in polymutt denovo output.
Merge branch 'master' into gb_master
removed testing code
many times faster indel readcounts by using mpileup -r
cache file for the UR class browser
command_class_name is what was wanted anyway

id was not always the command class name, luckily there's a
command_class_name field!
hide color when STDOUT and STDERR are not TTYs

When piping or `watch`ing commands that use this the color escape codes
would be visible.  I don't know if this is the best way to do this but
it seems to work.  Since we only have the string we are assuming we
should disable color if either STDOUT or STDERR are not TTYs.
updated ur submodule to ca16655
bless somatic-validation-sv additions snvs.detailed.vcf
removed bad database entity creation from DGIDB RussLampel importer
updated ur submodule to 60d4d22
Add a header indicating origin to BAMs including only internal data.

This is currently hard-coded to the string:
@CO This sequence data was produced in Saint Louis, Missouri, USA.

For anyone outside the city this should hopefully be configurable.
Updated `genome` tab completion.
Updated `gmt` tab completion.