Patch: Do not clean up all simulations all the time

The enclosed patch disables the global cleanup calll, and instead cleans up individual simulations as they are submitted.

It also removes the "finished" attribute of restarts, which is not really necessary since one can instead look for the "*-active" symlink.

It re-organises the code internally somewhat, as the current code assumes that restarts in the "U" (finished) state do not need to be cleaned up any more.

In addition, it adds a set of TODO comments where the current code could be improved.

This patch probably conflicts severely with Michael Thomas's patch addressing the same issue; I propose to combine both patches in some way before committing them.

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