HPO archive of the ontology and annotations. Note, that all files are gzipped. The folder "2009-2013" is separated by month. The folder "2014-2015" has a folder for each week of the year.
The archives of the HPO (i.e. only the ontology) can be found in the folders "2009-2013" and "2014-2015".
The archives of the associations between HPO-classes and Disease can be found in the folders "2009-2013" and "2014-2015".
There was a job on hudson/jenkins that was called "hpo.annotations.monthly". I moved a lot of these builds into the folder "hpo.annotations.monthly", but not all.
The build numbers can be found in the corresponding "build.xml" file that should be contained in every build-folder.
If you have questions, contact dr.sebastian.koehler@gmail.com.