Jalview has a bug tracker which can be found here.
I found a bug with reading Stockholm files and I logged it there. There were a few Stockholm files from Rfam that I wasn't able to open. "\\" is used to denote the end of a Stockholm file, which coincidentally is found in urls! I fixed the bug by requiring that the line with "//" start with "//" or a space then "//".
After fixing this bug I decided to start a branch in my svn repository (just to try it out), but I found out that I did not do this correctly. The svn red book has a nice entry about branch philosophy. What you should do is copy the existing trunk into the new branch. This allows diffs to be created properly between different versions. For now I am not going to have branches since Jim is going to set up an official repository for Jalview later.