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.
packages.mk: remove '--disable-deprecated-symbols' flag for HDF5

Other tools (e.g. h5py) require these deprecated symbols.
dynamics: add tensor-valued custom correlation functions

In the user script, an additional parameter 'shape' must be given to
specify the extents of the result.

Tensors of general rank are supported by the implementation of
correlation_adapter. The conversion from a nested Lua table to
boost::multi_array of rank > 1 is still lacking, see
halmd/utility/lua/array_converter.hpp.

Move class correlation_adaptor to separate file.
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.
packages.mk: update several packages

Update the following packages to their recent versions:

    Boost C++ (1.56.0)
    Clang (3.5.0)
    GCC (4.9.1)

The patches for Boost C++ still apply smoothly, although the issues may have
been fixed in the meantime in a different way.
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. Use std::cref
throughout.
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.
io/logger: add note on deprecated boost::empty_deleter
lua converters: revert to boost::cref

Using std::cref causes a Lua error "Trying to use unregistered class".
The reason is that luaponte (luabind) is C++98 and binds only
boost::cref, see libs/luaponte/luaponte/detail/convert_to_lua.hpp.

The bug was introduced in commit:4b16bd3, which was not properly tested.
This fixes #335919.
doc: update list of tested compilers
potentials: drop unneeded include of Boost.Assign

boost::assign::list_of was used to set default array parameters (e.g.,
the cutoff). This is now handled by the Lua scripts.
mdsim.potentials: move to sub-namespace "pair"

This prepares for the implementation of other potential types, e.g.,
external potentials.

The change breaks basically all simulation scripts, which can be fixed
by replacing "mdsim.potentials" by "mdsim.potentials.pair", etc.
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...
move from boost::array to std::array

As boost::list_of is not compatible with std::array, convert
construction from list_of to C++11 initializer lists.
C++11: move from boost::tuple to std::tuple
packages.mk: make compiler for Boost libraries configurable

The make variable BOOST_TOOLSET can take these values:
    gcc, clang, intel, pgi, ...
packages.mk: drop GNU Parallel

This program is not related to the build or development process of
HALMD.
doc: expand trouble shooting for building Boost C++

Further, update installation targets found in packages.mk.