Fixed TNG memory alignment problem and reset pointers.

This is a temporary fix to the memory alignment problems on some
platforms. In the main TNG repository the whole I/O system is
rewritten to address this problem. This fix is to avoid the
problems without making too large changes.

There are also some pointers that were not reset after memory
was freed. This is also fixed in here.

This commit does not correspond to any commit in the TNG
repository.

Fixes #1542, #1546, #1547 and #1559.

Change-Id: I90a6406cccbc43fd57d4423c2b661019cf7763e8
Fix zlib usage with TNG

Using zlib for TNG requires also that the the #include file can be
found, and this can be in a non-standard path. One part of this commit
should be rolled back into the TNG repo.

Change-Id: Iaa70ddd4f5471e405404148e6e83067d5ea52a27
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
Generalize markdown configuration machinery

This implementation scales a bit better as we increase the number of
markdown files. It may even be easier to understand! Preserves
existing top-level targets, and general behaviour. The full ARGN
functionality is not yet used, but it will be shortly.

Introduced stub user guide, with HTML and PDF build.

Change-Id: I198f273a08f81035694c3efefd35a5b2f2af7f0d
Backport of 'Remove unused figures from share/html/'

from master branch. Some of the flowchart images are also unused, but
left them there for completeness.

Change-Id: Ia47f9ac62f865f60c6f1998f407d62c9ba6c66f2
Initialize unused velocity constraint components

With domain decomposition, velocity components for communicated
atoms could be uninitialized. These components were never used, but
this could lead to valgrind warnings and floating point exceptions.

Fixes #1576.

Change-Id: Ic673680699578ddf62c2d240342138cbc16490c8
Merge release-5-0 into master

Conflicts:
	install-guide/configure-install-guide.cmake.in
		applied to docs/configure-markdown.cmake.in
Moved doxygen/cycle-suppressions.txt -> docs/doxygen/cycle-suppressions.txt
docs/CMakeLists.txt: replaced PROJECT_VERSION with GMX_VERSION_STRING

Change-Id: I61724a10a5331fdf747edd411dfa2f2256cd3f6b