packages.mk: update several packages

Update the following packages to their recent versions:

    LuaJIT (2.0.2)
    HDF5 (1.8.11)
    Clang (3.3)
    GCC (4.8.1)
    Git Annex (4.20130723)

Consistently use macros for external programs.

The update follows git://git.colberg.org/packages.git, which is
maintained by Peter Colberg.
packages.mk: drop stuff that is unrelated to HALMD

The following packages are dropped:

    htop
    Bootstraping GHC (Glasgow Haskell Compiler)
    GHC (Glasgow Haskell Compiler)
    Haskell Cabal
    PCRE (Perl Compatible Regular Expressions)
    git-annex

Further support may be found at git://git.colberg.org/packages.git.

Fix URL for nvcuda-tools and move version to latest commit.
packages.mk: install CMake-CUDA from tar ball

This approach is more in line with the other packages and avoids
checking out the whole Git repository.
packages.mk: move Boost to version 1.54.0

This version contains Boost.Log for the first time, which will allow us
to drop this explicit dependency soon.

The included patch for Boost.Log is found at
http://www.boost.org/patches/1_54_0/003-log.patch

Add a switch BOOST_ABI to select the C++ mode of compilation. HALMD
0.2.x requires still C++98.
lua: support 'memory' parameter for particle and Lennard-Jones

The memory parameter can enforce the variant of the particle module.
Previously, if there was a GPU available, it was used automatically and
the only possibility was to deactivate it via '--disable-gpu' parameter
at the halmd command line. With the optional 'memory' parameter this can
be controlled now at a script level.

Furthermore, make the Lennard-Jones potential module aware of the
attribute of the particle instance.
potentials/morse: revise c++ modules

Drop deprecated module_name() function, replace get() methods by
boost:tie().

Remove 'using namespace' for readability and forward-compatibility.
potentials/morse: revise Lua module

Document the potential formula, remove deprecated module functions and
use 'memory' parameter from particle instances to use the correct
implementation.
lua/pair_full: update lua module and document it

Make the pair_full potential work with the new lua interface and
document the module usage.
lua/pair_trunc: correct get_net_force() documentation

get_net_force() was incorrectly documented as get_force().

Make use of utility.assert_kwarg()
host/pair_full: Do not count the interaction twice