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