- enable interaction of two larger-than period bodies (e.g. cylinder vs. box) in addition to previous commit.
- point to the "allowBiggerThanPeriod" flag in the LOG_FATAL message.
Fix compilation with boost >=1.47
Added google analytics script to sphinx doc
DomainLimiter:
* Delete spheres only
* Add mass calculation
* Add volume calculation
* Add mask-parameter

SpheresFactory:
* Add color parameter
- improvements in TW interface so that one can save and load "state" files to be used for defining deformations (this will actually be used by E. Ando for analyzing experimental data!)
- code cleaning
- make deformation analysis possible for arbitrary simulations (no longer depends on TriaxialEngine for defining the bounds)
- fixed undefined variable when Triaxial engine is not present
- erase bodies before adding spheres from file
1. fix some typos
2. derive WirePhys from FrictPhys
3. compute limitFactor for WirePM
4. add limitFactor and normal force of wires to wpm in VTKRecorder
Add mass-parameter to VTKRecorder.
- Fix typo (thanks for pointing out Klaus, actually the "i" was correct: elastic-plastic means that the law is incrementaly elastic OR plastic, while elasto-plastic laws can be both at the same time)
- big reorganization of the triangulation lib, which becomes a template library. Usage of different "info" classes for different engines is now possible, so that TWrapper doesn't have to instantiate useless variables inherited from the flow problem, and vice-versa. Will also worj for periodic flow model coming soon.
- general code cleaning and removal of old files
- a few hyperlinks fixed in *.bib's
- remove custom dependencies breaking compilation
Update some publication references
Merge the "collide" branch to trunk (branch history at https://code.launchpad.net/~bruno-chareyre/yade/collide2)

Summary:
- the stride logic is improved by using displacements instead of velocities. Reference position and sweepLength are added to bounds.
- the sweepLength of each body is updated in collider::action() according to collider's targetInterv, so that ideally all bodies leave their bounds at the same iteration (more or less the same idea as in the old velocityBin but with per-body logic)
- a number of optimizations in the collider and interaction dispatcher. Namely, the handling of virtual interactions is a lot faster, allowing a larger number of them for the optimal verletDist.
- timings reported at https://yade-dem.org/wiki/Colliders_performace (please add your reports there), roughly x3 speedup vs. bzr2999 in triaxial simulations
- A new ZECollider is introduced, using CGAL's dD intersection algorithm. It is relatively slow and therefore not recommended, but the code is very short and it may be worth a try when parallel CGAL is released.
- Added references to some CGAL packages and a few fixes in references.
- missing reference update
- remove the velocityBins lines in tests since velocityBins are removed from trunk
- add capability to deactivate the damping in NewtonIntegrator for individual particle via O.bodies[id].state.isDamped=False
- use this new property in examples/WireMatPM/wirecontacttest.py
- Draft version of the periodic fluid model from Donia Marzougui
smallfix in flow model