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Remove Run-2 rerun options and some obsolete jobOptions

Stewart Martin-Haugh requested to merge smh/athena:rerunLVL1 into master

In run 3 we use "doL1Sim=True" to rerun the L1 simulation on bytestream, so these options are no longer needed. I also removed jobOptions only referenced in those options, and removed some other obsolete jOs.

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