* 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.
