FIX:annotation semantics: adresses #1283

I followed the logic of the discussion in #1283: changed the names of read_annot write_annot to match the pattern we established. I also changed _read_annot to read_annot (and did the same for _write_annot).
@christianbrodbeck because these names are already too long.
@Eric89GXL though this completely violates the expected ordering and logic of the very packages files we are using here