Cleanup of simulation code#12

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sw wants to merge 8 commits intotriffid:masterfrom

Commits on Oct 18, 2010

Commits on Oct 20, 2010

Merge remote branch 'upstream/master'
sw
committed

Commits on Oct 21, 2010

Merge remote branch 'upstream/master'
sw
committed

Commits on Oct 23, 2010

Merge remote branch 'upstream/master' into sim_plot
sw
committed
Move simulation code into simulation/ directory. Fix timers in simulation. Clean up firmware code.
sw
committed

Commits on Oct 30, 2010