Over the summer the JBrowse project has been very capably assisted by two student interns. In Toronto, Natalie Fox has been working on extending the JBrowse user interface and feature set, while in Berkeley, Stephen Cummings has been documenting the existing server-side API. You can track their efforts via the links above, which lead to the GMOD wiki (the new home of JBrowse documentation).
The debt ceiling and budget kerfuffles seem to have delayed things in Bethesda somewhat, with the ripple effect of delaying our process of hiring someone to fill the JBrowse lead developer position, but we hope that will all be resolved soon (watch this space). In the meantime, check out the progress that Natalie has made with faceted browsing and hierarchical track organization -- it is really exciting, and in fact seems quite obviously crucial, as genome databases naturally progress to having hundreds and even thousands of experimental annotation tracks.