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.