update SCM code to use latest CCPP main branches

[grantfirl]

This updates the SCM to use the latest CCPP physics/framework main branches and addresses some issues pointed out be @egrell :

• fixes some mistakes in the Users' Guide
• add the timestep and output intervals to the run script output
• fix a typo in the run script

[ligiabernardet]

I incorrectly labelled his PR as needed for CCPP v6. I see this pertains to main. So I have not removed the CCPP v6 label. Sorry for the confusion.