Revert "fixes for GFF3; going to branch to revert to GFF2 support"

This reverts commit 9e89346d430db6b535f09c42c28c50b823d0418b.
Revert "GFF3 work"

This reverts commit 4f465553c2ec8e017ec375cc7c6f123b9699a9ed.
Revert "GFF3 converstion work"

This reverts commit be6f6113838221bb8d77f71f5b6ee69ba6fab70c.