Of the 103 wrapper files generated by SWIG, I've managed to get 58 to compile. The rest rely on Tree objects, with which I've had trouble. One issue--one of the objects (TreeTools) has a function that returns a structure whose definition is nested within the TreeTools class. SWIG doesn't support this, though it's on the list to be supported in a future version. I think the best thing to do there is to just remove that structure and the one function, in wait for the future version.
Otherwise, I'm having issues with templating. I have one templated function that calls another in the file TreeTemplateTools. And for some reason, SWIG isn't able to find the inner function. I've posted to both the SWIG and GSoC mailing lists, and hopefully I'll get an answer.
Pjotr also asked me to move the SWIG interface files to a biopp subdirectory, to mimic the directory structure of the other projects. This was easily done.