Hi Jan.
It's good to see the updates to your project proposal on the PhyloSOC wiki:
http://informatics.nescent.org/wiki/PhyloSoC:_Extending_Jalview_support_for_handling_RNA
You should also start putting in a few more details about the exact classes and functionality involved. When we skyped, we talked about you creating new issues in the bugtracker at issues.jalview.org relating to each stage of your project - so in your first week, you could provide a link to JAL-826 (http://issues.jalview.org/browse/JAL-826) which is the master bug related to the code merge.
Finally, as you start committing code to your clone of jalview.git, remember to mention any associated jalview bug ids (e.g. JAL-826) - this means that the 'Git commits' tab on bug JAL-826 will list all the commits mentioning its ID, which makes it easy to see what has been done for that issue.
Jim.
ps. still working on the certificate host name problem for source.jalview.org - hoping it'll be sorted out before I get on a plane tomorrow evening!