Revert "Revert "create a dummy expected output file as standard for cnv detectors""

This reverts commit 5abef98c7ca3d5782240449500339ead9fc2b03e.
Revert "Revert "fix up some copy pasta error messages""

This reverts commit 6055056b0dba9c93204e845b582a5f213384acdd.
Revert "Revert "write our temp files to a reasonable place""

This reverts commit 3cd0df3a9b7e6715ec16ea6cf02ef7706778bbbb.
Revert "Revert "do the right thing with the copycat annotation""

This reverts commit e06fc4e36dd8092fee0b1f22eb730ce3a5a6ac8d.
handle annotation data set correctly in the test
note the annoation-version param is deprecated