Merge pull request #5 from rjleveque/rjl

Many updates to 5.0 documentation
Initial add of PyClaw docs.
split up setrun documentation into clawdata and amrdata parameters
started listing changes from 4.x to 5.0
Fixed error in installation instructions for make_clawtop.sh,

it's a bash script, not python, and ln -sf doesn't work for directories
added restart.rst on checkpointing/restart
discuss restart in setrun.rst
added restart description, fixed setrun example for classic
Removed many unused files and reorganized index, added pyclaw/index to main index
fixed merge problem after rebasing