Unify documentation for webpage build

Unify documentation for webpage build

The new webpage build can be run either from a code repo (for
development), or from the unpacked source tarball (for actual
deployment). The latter is useful to ensure the documentation reflects
the tarball, and because the tarballs and their md5sum values must be
available for building the webpage. A Jenkins flow job can build the
tarballs and then construct the webpage for automated delivery. The
machinery is active only if GMX_BUILD_WEBPAGE is set (and other pieces
in place), so will be transparent to normal users.

Created configurable top-level index.md inside the new docs top-level
directory. Various components have moved into this directory, but each
can still be built independently.

Imported some basic (but pandoc-specific) CSS from
https://gist.github.com/ryangray/1882525

Made a new top-level index.md, and made it build HTML with Pandoc and
use the CSS. Later, we can consider making the whole static site build
work with some generator, e.g. to make links automatically.

Established CMake variables for configuring the webpage build with
the names of tarballs and their md5sum values. Builds from the repo
don't include this part of the webpage.

Moved the install guide into the new docs directory. Minor fixes to
header levels. Generated PDF install guide also. Used
PANDOC_EXECUTABLE instead of hard-coded "pandoc."  Made it use the
CSS.

Moved reference manual build into the new docs directory, and linked
its default setting to GMX_BUILD_WEBPAGE.

Moved old html guide content into the new docs directory. This still
installs in the old way. Fixed broken links for xpm2ps and grompp.
Added rudimentary hdb.html to fix missing link target. Removed text
that linked to ancient material that no longer semes to exist.

Moved doxygen generation into the new docs directory. The useful
output now goes directly to build/docs/html, and logs to
build/docs/doxygen.

Bumped copyright years to keep uncrustify script happy.

Bumped top-level CMakeLists.txt and CPackInit.cmake to check for the
new correct paths when building tarballs.

Added config file for linkchecker to help automate checking
the links all work.

Refs #1242

Change-Id: I8e5cf98b2997b76f56b24f45262c9c9eebf9900e