packages.mk: update several packages

Update the following packages to their recent versions:

    Lua (5.2.2)
    Git (1.8.4)
    GCC (4.8.2)

Encode inline patches using base64 to avoid inconsistencies with regard to
escaping with different versions of GNU make.

Install GMP header files to include directory for GCC plugins. Retrieve
GNU MP from http mirror.

The update follows git://git.colberg.org/packages.git, which is
maintained by Peter Colberg.
packages.mk: fix lib path in GCC prerequisites

If libdir is omitted during configuration, it is either lib or lib64
depending on the architecture. Then packages depending on GMP, PPL, ...
do not find the respective libraries.

The issue appeared on OpenSuSE 12.3 and may be related to
http://gcc.gnu.org/bugzilla/show_bug.cgi?id=53798.

In cloog-ppl, adding linkage against libm.a resolved the following
error:

ld: .../.ppl-0.11.2/lib/libppl.a(Init.o): undefined reference to symbol 'fegetround@@GLIBC_2.2.5'
ld: note: 'fegetround@@GLIBC_2.2.5' is defined in DSO /lib64/libm.so.6 so
try adding it to the linker command line
/lib64/libm.so.6: could not read symbols: Invalid operation
add test modularity/two_particles

The purpose of the test is to check the usability of several particle
instances. The scripts setup, equilibrate, and simulate a binary mixture
where each species is kept in a separate particle instance.

Creating particle instances from subsets of particle is not yet
possible. Even a workaround in Lua via observables.phase_space is
prohibited since the data slot returned by acquire() can not be called
from Lua. Another possible workaround would use {set,get}_{position,…}
and extract the data (nested tables!) by hand. (Which I'm not going to
implement in Lua.)

Actual checks of the final result are missing though.

This commit refs #198261.
remove dependency of potentials on mdsim::particle

C++ classes: drop explicit specification of number of species types in
the constructor. These numbers are implied by the shape of the parameter
matrices.

Check matching parameter matrices and number of particle species in the
constructor of the force classes.

Lua: provide optional parameters "species", "memory", and "label"
instead of the dependency on an instance of mdsim::particle.
observables/sampler: reintroduce on_prepare() signal

After being removed in commit 9360386, it is needed for the new forces
implementation again.
WIP: revert commit bb52a29
particle: create signal on_force()

This signal is supposed to inform the force module about (possibly)
necessary force updates. The forces will then test with the caching
mechanism if a force update is required or not.

This adds a (small) overhead when requesting auxiliary variables or the
force itself as every connected force module has to test whether to
update the variables or not.
progress update for force redesign

- move on_prepend/append_force to particle
- use on_prepend_force() for checking if a force update is required
- on_force() will be only called when any of the attached force module
  needs an update
- throw an exception if aux_enable() was not called and auxiliary
  variables need an update, the intention is to prevent calculating the
  force twice