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21.9: Update RunUpgradeTests.py to add new mode for "in development" changes

Nicholas Styles requested to merge nstyles/athena:21.9-testUpdate into 21.9

Update RunUpgradeTests.py to add new mode for testing in development changes, as basis for future baseline.

The -u option uses an updated transform command (currently only defined for simulation) which allows testing of the commands necessary for running with the planned naming scheme/ID scheme updates.

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