Small adjustments and clean up.
 - Adjusted ForceCalculator_LennardJones::compute().
 - Edited example logging configuration file "MolSim.logging.conf":
   Logging messages now print less prefixes.
 - Moved input files in new directory "examples/".
Implemented XML input and revised input/output methods.
 - Parameters for simulation and I/O are now read from a XML file.
   This replaces direct command line input.
   More parameters can now be specified.
 - ParticleInput classes now use std::list<Particle> instead of ParticleContainer.
 - Added global variable "output_freq" to specify output frequency.
 - Created example XML files.