Tweak the doc build process

I moved all documentation sources (guides, manuals, etc) to `src/doc` to free up `doc` as a build directory for all generated files.

At the same time, I also removed our usage of `VPATH` from the makefiles because it was wreaking havoc with doc deps and it's not very necessary now that we're primarily a rust project rather than having a good portion of C++/C inside of it.