Documentation enhancements

What should be documented but is not currently

• O.bodies.erase in the user's manual
• python returning by reference vs. value, handling of sequences, why del O.engines[3] does not work etc etc.
• batch system and --gnuplot (https://lists.launchpad.net/yade-users/msg03724.html)
• collider optimization (verlet distances): https://lists.launchpad.net/yade-users/msg03725.html

flow engines on ubuntu 12.04