Yes those are the same GFF files. If you are using an FTP client, not a browser, you can see that the species directories under each release directory is a symlink to the location in genomes. They do not contain the FlyBase release tag because not every species will be updated with each release. For example, the FB2008_06 directory links to species from the FB2008_05 release. We felt including a mix of FlyBase release numbers, not the species annotation release number, under a tagged release directory would be confusing.
The presence of the older GFF files is explained in ftp://ftp.flybase.net/genomes/Drosophil ... /Changelog
. Please let us know if you have further questions. We try not to update files mid release but this one was enough of a problem that it couldn't wait until our next release cycle.
r5.10 refers to the 10th version (there wasn't a public r5.0 release) of the release 5 assembly for Drosophila melanogaster. The change from 5.9 to 5.10 signifies that there were gene model changes. It was released as part of FB2008_07 which refers to the 7th release of FlyBase in 2008. FB2008_07 also contains r1.3 of Dana, Dere, Dgri, Dmoj, Dper, Dsec, Dsim, Dwil, and Dyak, Dpse r2.3, and Dvir r1.2. Is this what you were asking?