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
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
Merge pull request #6 from rjleveque/rjl

Merged pyclaw documentation into doc/doc and cleaned up old files