examples: adjust "patch_h5md_for_VMD" for 2D data

The VMD plugin can't yet handle 2D data. Thus we extend them to 3
dimensions by hand, putting z=0.
doc: fix Unicode character for apostrophe

cd doc/pdf && pdflatex halmd.tex:

! Package inputenc Error: Unicode char \u8:ʹ not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...

l.8973 \emph{HALʹs MD package}
                                is maintained in a public Git repository. \h...
doc: fix signs for pressure, virial, and stress tensor

The change affects the documentation only. The signs are correct in the
implementation.
doc: revise installation instructions

* add subsections in the list of prerequisites

* mention a C++11 compiler first

* a system installation of Boost C++ won't do it

* builds without GPU support are possible

* mention LuaJIT as an alternative to Lua

* require Sphinx ≥ 1.2

* drop section on AIX
  (We're not going to run HAL's MD package on AIX.)
packages.mk: update HALMD to 1.0-alpha2

Download the tarball from halmd.org and verify its signature.
lua: fix FTBFS with Boost C++ 1.56

The move constructor of boost::cref has silently been dropped for
compatibility with std::cref:
https://svn.boost.org/trac/boost/ticket/10368

This breaks code such as "cref(v[i])" found in some Lua converters.
Rewrite the for-loops to avoid such constructions.
host/potentials: fix uninitialized memory for cutoff energy

In order to calculate the cutoff energy, the functor of the potential is
being called upon construction of the potential -- but without
initializing en_cut_ properly to zero, causing incorrect cutoff energies
and occasional failings in the tests, e.g.:

http://my.cdash.org/testDetails.php?test=14241015&build=584152
http://my.cdash.org/testDetails.php?test=16653293&build=668443
http://my.cdash.org/testDetails.php?test=16666513&build=668912

All host potentials were affected by this bug, but GPU backends are not
affected, as these initialize the cutoff energy differently.

Fixes #283787
Merge branch 'testing'

The merge was necessary due to a critical bug in host/potentials.

* testing:
  host/potentials: fix uninitialized memory for cutoff energy
  lua: fix FTBFS with Boost C++ 1.56
  packages.mk: update HALMD to 1.0-alpha2
  doc: revise installation instructions
  doc: fix signs for pressure, virial, and stress tensor
  doc: fix Unicode character for apostrophe
  examples: adjust "patch_h5md_for_VMD" for 2D data

Conflicts:
	halmd/mdsim/host/potentials/pair/lennard_jones.cpp
	halmd/mdsim/host/potentials/pair/modified_lennard_jones.cpp
	halmd/mdsim/host/potentials/pair/morse.cpp
	halmd/mdsim/host/potentials/pair/power_law.cpp
	halmd/mdsim/host/potentials/pair/power_law_with_core.cpp