Integrate initial setup into main run routines

[shyamamrith]

This could run each time Simstock is run. The initial setup is generally fast to run, especially after it has been run once before. Alternatively, if all tests have been passed, this could be recorded in a log file that is checked each time.

Making this change would avoid requiring the user to remember to run the initial setup, which could be especially useful after issuing updates to the plugin.