fix compiler warning on signed/unsigned comparison

The warning is given by GCC 4.7 with Boost 1.53.0 and is reported as a
build error, see http://my.cdash.org/viewBuildError.php?type=0&buildid=585601

In file included from /local/modules/boost/include/boost/test/unit_test.hpp:19:0,
                 from /.../src/test/integration/validation/thermodynamics.cpp:23:
/local/modules/boost/include/boost/test/test_tools.hpp: In Instanziierung von »boost::test_tools::predicate_result boost::test_tools::tt_detail::equal_impl(const Left&, const Right&) [mit Left = int; Right = unsigned int]«:
/local/modules/boost/include/boost/test/test_tools.hpp:560:40:   erfordert durch »boost::test_tools::predicate_result boost::test_tools::tt_detail::equal_impl_frwd::call_impl(const Left&, const Right&, mpl_::false_) const [mit Left = int; Right = unsigned int; mpl_::false_ = mpl_::bool_<false>]«
/local/modules/boost/include/boost/test/test_tools.hpp:575:56:   erfordert durch »boost::test_tools::predicate_result boost::test_tools::tt_detail::equal_impl_frwd::operator()(const Left&, const Right&) const [mit Left = int; Right = unsigned int]«
/local/modules/boost/include/boost/test/test_tools.hpp:523:1:   erfordert durch »bool boost::test_tools::tt_detail::check_frwd(Pred, const boost::unit_test::lazy_ostream&, boost::test_tools::const_string, std::size_t, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, const Arg0&, const char*, const Arg1&, const char*) [mit Pred = boost::test_tools::tt_detail::equal_impl_frwd; Arg0 = int; Arg1 = unsigned int; boost::test_tools::const_string = boost::unit_test::basic_cstring<const char>; std::size_t = long unsigned int]«
/.../src/test/integration/validation/thermodynamics.cpp:69:1:   von hier erfordert
/local/modules/boost/include/boost/test/test_tools.hpp:536:20:
doc: clarify documentation of potentials

local_r4: make clear that the potential is shifted before the smoothing
          function is multiplied

          use 'g' rather than 'f' for the function to avoid potential
          confusion with the force.

lennard_jones_linear: fix typo
io/writers/h5md: allow for non-decreasing time dataset

This relaxed condition corresponds to H5MD 1.0.1 and allows us to change
the state of the simulation without incrementing time, e.g., rescaling
of the velocities.
avoid exception in H5MD output of trajectories

If the sampling interval is omitted in the phase space writer, a dump of
the system state is triggered by the signals "start"and "finish" of
observables.sampler. These two signals are always emitted by
sampler:run(). Repeated calls lead to duplicate dumps at the _same_
simulation step, which is not valid H5MD.

The following workarounds are possible:

1) remove the signals "start", "finish" from sampler:run()

2) increment the step counter (but not the clock) after each call to
   sampler:run()

3) avoid connection of the phase space writer to start/finish by
   explicitly passing a sampling interval, e.g., the total number of
   simulation steps.

This patch applies the last option and fixes #286246.
doc: fix module path in example
forces/pair: add weight parameter for auxiliary variables

In the case of different particle instances it can be useful to
calculate the full potential energy (and not only half of it) for one
particle instance (AB) and disabling it completely for the other (BA).

This commit closes #265536
cmake: make potentials (except lennard_jones) optional

As each potential increases the build time significantly, make them
optional. This is especially useful for development, as in most cases
only one potential is actually required.

Always keep the Lennard-Jones potential because it is required by the
thermodynamics, local_r4 and the verlet_nvt_hoover unit tests.
cmake: use one list to switch potentials on or off

As the number of potentials grows, a single checkbox for each one will
clutter the CMake configuration file. Instead we use a single list which
is used to define non-cached variables HALMD_WITH_${potential} in the
top-level CMake script.

Drop the special treatment of the Lennard-Jones potential. Disable tests
which link against this potential. (Script-based tests will fail if
LJ is disabled.)

lua: Copy only these potential modules which are enabled

doc: FIXME The doc still resorts to the Lua files in the source tree and
     not in the build tree. (I suppose that the order of execution of
     the various CMake subdirectories is undefined.) Thus the
     documentation will still list disabled potentials as well.
install Lua files in share/halmd/lua/halmd/

Before the files were copied to share/halmd, i.e., to the top-level
directory of common halmd files. The trailing "halmd" is needed by Lua
such that all modules are in the namespace "halmd".
doc: add step-by-step guide for Ubuntu 14.04
doc: give the HTML theme a fresh look

Inherit from agogo theme, let sidebar move upon scrolling.
doc/readme: revise introduction, add links to module sections
doc: add links to doc archive
doc/installation/ubuntu: fix ReST syntax error

doc/installation/ubuntu.rst:65: WARNING: Inline literal start-string without end-string.
add doc archive to sidebar
doc: make TOC scroll properly
doc: use better fonts, minor layout changes

halmd.css_t: add missing style "p.rubric"
doc: minor changes
doc/readme: mention Nicolas Höft explicitly
doc: include develop.rst in TOC tree

Let the developer guide start with this overview.

Rename directory developer/ to develop/