Revert "do the right thing with the copycat annotation"

This reverts commit 65dbe38a62362bdea69937309a585340ae60fa5f.
Revert "write our temp files to a reasonable place"

This reverts commit e30cd6f01e8a48a1bb624f6a4835b23ba410b148.
Revert "fix up some copy pasta error messages"

This reverts commit 2c1accd40beae7891fab44091ad819e16149f18d.
Revert "create a dummy expected output file as standard for cnv detectors"

This reverts commit 5041fff7478e7dd4211d9bde52898c2bbf70262b.
updated ur submodule to b0d8d06
updated workflow submodule to d7e2b3b
Add additional message about viewing progress
Add _link_process function
rex_process_link/start scripts pass on all arguments
Capture stderr as well as stdout in Park::Base::_run_generic_process
Add gmt cross-sample indel command

This command uses the Park system under the hood.  The tests only test
up to that handoff.
Add summary_threshold to WorkflowMixin (genome model build view)
Allow --logs to be separate from --workflow in WorkflowMixin