Implement user guide

Implement user guide

Renamed former user manual to reference manual.

The content for the new user guide has mostly migrated in from the
wiki, install guide, and mdrun -h, and updated as appropriate. This
guide is intended for documenting practical use, whereas the reference
manual should document algorithms and high-level implementations, etc.

Established references.md to do automatic linking of frequently
used things. This can be automatically concatenated by pandoc
onto any Markdown file to do easy link generation.

Section on mdrun and performance imported and enhanced from the
Acceleration and Parallelization wiki page.

Added section on mdrun features, e.g. rerun and multi-simulation.

Section on getting started imported from online/getting_started.html
and updated - there used to be a tutorial here, but there isn't any
more. Linked to more up-to-date tutorials.

Added TNG to docs/manual/files.tex.

Removed gmx options, now that its content is in the user guide (in
tools.md).

Moved old mdp_opt.html to docs/mdp-options.html, for now. Removed from
reference manual, left pointer to new location. This is not an ideal
format or location either, but it's a step closer to being able to
generate it from the code. Some trivial fixes to content. Generating
links and references to follow in a future commit.

Moved environment-variable section from reference manual to user guide.
Minor fixes here.

Removed superseded reference manual sections on running in parallel or
with GPUs. Renamed install.tex as technical-details.tex, because that
is all that is left there. Moved section on use of floating-point
precision to chapter on definitions and units, and thus eliminated the
former Appendix A.

Cross-references from user-guide.pdf don't work well yet, but that
should be dealt with when we decide on the final publishing platform.

Some TODO comments for documentation sections remain for work in
future patches, but please note the other new content in existing
child patches, so we don't duplicate any work.

Change-Id: I026d67353863ae069c6c45b840a61fcaf205a377