Move doc/ to src/doc/

We generate documentation into the doc/ directory, so we shouldn't be
intermingling source files with generated files
Remove VPATH usage in Makefiles

This is just messing up all the doc dependencies because of such similar
directory names and file names.

Closes #11422
Rewrite the doc makefile for doc => src/doc

This continues to generate all documentation into doc, but it now looks for
source files in src/doc

Closes #11860
auto merge of #11891 : alexcrichton/rust/docs, r=brson

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.