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.