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Repurposed -OO for all sim run outputs including S_sie.resource being saved in the specified directory. (#1714)

* 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.

35 of 39 new or added lines in 3 files covered. (89.74%)

12289 of 21990 relevant lines covered (55.88%)

79736.88 hits per line