remove annot class in favor of SeqSpan

It's not quite as clean as I might like as my metadata Annotations class
is annoying to access in C++.

also to support our our "legacy" mussa annotation file format I added
a couple of annotation creating helper functions.

Since I didn't want to also change the motif class at the same time,
I just move the members of annot into motif. At some point I'll finish
getting ride of motif.