Remove UR_DBI_NO_COMMIT from TestHelpers.pm

since all .pm files are loaded by commands as they search for
sub-commands, we cannot put this in TestHelpers.pm.  It would be a nice
thing to have there since it would stop people from putting test
entities into the database by accident, but until we can safely put it
there it should be removed.
Rename TestObjGenerator
Merge branch 'fireteam2' into gb_master
Add an alias individual_common_name to expected_common_name so Solr finds it.
add top level config command to tab completion
allow null alternate alleles in Genome::File::Vcf::Entry
bugfix: dereference arrayref in Vcf::Entry::genotype_for_sample
Initial version
Check in perl script as gmt
Make it clearer
Make global variables for parameters
Make it clearer
Fix formatting
Fix formatting
Only deal with one bedpe file
Global constants for parameters
Remove complexity from single-sample version
Initial change to gmt and add test
Merge branch 'fireteam' into gb_master
add environment variable to declare the root directory into which different GMS systems attach, when attached