What files/directories to commit

I recently had some issues with the way I was committing my files. Normally I commit everything from the root of trellis. Should I commit everything or should I only commit the sites files? Thanks in advance for any advice you might have here.

What do you mean by this?

You could reference GitHub - roots/roots-example-project.com: Example Roots stack project (Trellis, Bedrock, Sage)