-- in the simulation window, what means the options:
Do not deploy the Flow
Do not run repository content command after Flow deployment

* When you do a simulation differents steps are followed:
1-the simulation repository content is cleaned
2-the objects are deployed in the simulation repository
3-the repository content is checked to verify all required objects are present in the simulation repository
4-the simulation itself runs
5-results are displayed

* The "Do not deploy the Flow" option means steps 1 and 2 are not done. It can be useful if you make tests and didn't modify your business documents, maps, flow, ... since last simulation if simulating the same map/flow. Or if you just modified the input file after previous simulation.

* The "Do not run repository content command after Flow deployment" means step 3 is not done

The purpose of these 2 options, that needs to be used carefully, is to speed up the execution of the simulation by skipping useless steps(it's to the user to advise when they are useless).