Just in case anyone is still interested, I have started an ensj (Ensembl Java API) project at sourceforge, using the latest version of the ensj-core project as the root of the fork. It fixes at least one bug with using the java API on hg19, and makes some improvements to the code for compatibility with java 1.6.
There are another few thousand changes I could make, but I’m just working on it slowly, if at all.
I’m not intending to support this full time, but interested parties are welcome to join the project and contribute, making this a truly open source version of the ensembl interface. That is to say, community driven.
Ensembl isn’t interested in providing support (they no longer have people with the in-depth knowledge of the API to provide support), so please don’t use this project with the expectation of help from the Ensembl team. Also note that significant enhancements or upgrades are unlikely unless you’re interested in contributing to them! (I have my own dissertation to write and am not looking to take this on as a full time job!)
If you’re interested in using it, however, you can find the project here: