You can clone with
HTTPS or Subversion.
Currently the documentation includes all the classes that exist in the project.
In case of library project the documentation is better to be generated only for .h files that are included in "Copy Files" build phase.
Not a perfect solution (it doesn't take into account the "Copy Files" build phase), but I'm using
$ appledoc [options] $(find Classes -name '*.h')
and it is working just fine.
Appledoc works on paths, so as long as you can move those files into separate folder, you can set it to only parse those.