Added real-time library to linker flags

Since last commit, real time functions are used to generate the seed. Some linkers need explicit command to include the corresponding library.
Do not read comments from in-files
Fixed some implicit type conversions
Fixed infinite loop when integrator step size overshoots particle lifetime
Improved progress display
Bugfix: invalid initial velocity was generated when using "customvol"
Added error message, when user defines invalid solid IDs in geometry.in
Completely refactored TParticle class.
Complete particle track is kept in memory, which allows the integrator
to pause, continue, restart from arbitrary points etc and more flexible
logging.
New feature: Initial energy spectrum for particles is read from
particle.in and parsed by "muparser"
Updated nr3.diff
Removed the redefinition of the throw statement in nr3.h which led to problems with muparser
Some optimizations and more detailed README
ODE stepper is resetted after trajectory change, speeding up integration quite a bit
More robust geometry collision point iteration
Some more information in README
Use CGAL library for geometry collision detection
Bugfix: minimum total energy was calculated incorrectly when using volume source
Fixed nr3.diff
Fixed nr3.diff
Some CGAL fixes
Fixed CGAL collision detection if segment-triangle-intersection result is a segment and not a point.
Added example include and lib paths to Makefile for manually compiled CGAL library.
Commented out usually unneeded Makefile variables
Improved description on how to manually include CGAL library.
Reverted some things from commit
8486ad756764f9408e9d5abb548241a769ade79e
Track cannot be kept in memory, takes too much space; moved logging back
into TParticle class.
Instead added particle type specific logging options.
Removed muparser from repository, assuming the user will install it
himself.
More flexible sources.
New object oriented sources to allow easier integration of new source
types.
Improved detection if a point lies within a solid body.
Missed source.h on last commit
Fixed search path options

Empty search path options broke some versions of gcc.