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* Repurposed -OO so all sim run outputs including S_sie.resource are saved to the specified folder. The files are placed in the sub-dir either RUN_xxx or DP_Product of the specified folder. * Updated for repurposed -OO. * Added quoting code markdown for such as in order to show <name> as is. * Added quoting code for missing items. * Updated to raise an error when the --read-only-sim flag is used without the -O or -OO. Also made updates to the related document accordingly. * Fixed the error message to be more clear.