Check Doxygen as part of Travis

I guess it depends what output we want to give the user. It may be failing to read a file, because its been excluded, as I found, which only shows up in stdout, hence you really want to show them everything. We could grep for warning, but that feels a bit hacky. We might be able to do something with tee, but it doesn't feel like it.

We could reverse the logic so it only runs make doxygen-doc a second time if it found errors.