Rename stage process to simulate, reconstruct, analyze

This allows for more granular control and better parallelization in the future (generate once, simulate multiple, reconstructed multiple, etc).

assigned to @wdconinc

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• 47b33adf - Also rename in single

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• fb1ca6d3 - Add finegrained scripts for single

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• 17e2f51b - Find common.sh in $(dirname $0)

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• a483882a - Write sim and rec files to sim_output

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• 1c3a4684 - Remove old all-inclusive single job

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enabled an automatic merge when the pipeline for 1c3a4684 succeeds

merged