misc: Fix BaseCPU doxygen

Doxygen was stopping with #include "arch/null/cpu_dummy.hh" so the html
for BaseCPU was only the three functions defined in the dummy CPU. This
forces doxygen to skip this #include correctly.

Note: The file references for base_cpu still aren't quite right, but it's
better than it was.

Change-Id: Ifafe247df2511caee2569d534bd29348a5ce9e8e
Signed-off-by: Jason Lowe-Power <jason@lowepower.com>
Reviewed-on: https://gem5-review.googlesource.com/11649
Reviewed-by: Brandon Potter <Brandon.Potter@amd.com>

Doxygen: Update the version of the Doxyfile

This patch bumps the Doxyfile to match more recent versions of
Doxygen. The sections that are deprecated have been removed, and the
new ones added. The project name has also been updated.

MEM: Put memory system document into doxygen

Fix up doxygen.

New directory structure:
- simulator source now in 'src' subdirectory
- imported files from 'ext' repository
- support building in arbitrary places, including
outside of the source tree. See comment at top
of SConstruct file for more details.
Regression tests are temporarily disabled; that
syetem needs more extensive revisions.

SConstruct:
Update for new directory structure.
Modify to support build trees that are not subdirectories
of the source tree. See comment at top of file for
more details.
Regression tests are temporarily disabled.
src/arch/SConscript:
src/arch/isa_parser.py:
src/python/SConscript:
Update for new directory structure.