packages.mk: update several packages

Update the following packages to their recent versions:

    Clang (3.4)
    GCC (4.9.0)
    Git (1.9.2)
    HALMD (1.0-alpha1)
    HDF5 (1.8.13)
    Lua (5.2.3)
    LuaJIT (2.0.3)
    luatrace (6150cfd: Feb 17, 2014)

Remove "GNU readline wrapper", which is not related to HALMD.

Fix output of "eval `make -f packages.mk env-PACKAGE`"

Update top-level targets.

The update follows git://git.colberg.org/packages.git, which is
maintained by Peter Colberg and distributed under the MIT license.
test/…/two_particles: fix script errors, make test pass

Due to the constantly failing tests, necessary changes in the interface
have not been detected.

Convert the enforced error message into an author warning, which can be
disabled by passing --Wno-dev to CMake.