MesoRD Code

First effort in getting the toolchain for building the user documentation into the cmake framework.

Worked on the buildscripts on linux

Addition of molecule-tracking for reaction in nearest neighbours, which also meant re-writing
a bit of the existing code to make it all look the same.
Worked on the compile time conditionals and fixed warningless compiles on OSX

Adding forgotten files

completed the cmake build script such that it works on unix like platforms. Made minor modifications to the code

Primarily work on microscopic homodimerization (which hopefully leads to a new release)

Tagging of the code used for MesoRD release 1.1 (from branch 1.0.1)

The molecule tracking module now provides a log file with the following information:

- length of a voxel (-q option)
- timestep between position outputs in trajectory.txt files (-w option)
- list of pairs of speciesnames and diffusion constants, in the same length & time units as used for the voxels and timesteps

More changes for allowing compilation on Unix systems via CMake.

Change of several files, especially the CMakeLists.txt files to allow compilation on Unix systems via CMake.