Thanks for the feedback. We would keep it in mind when we would be revamping the course. Clearly, I cannot cover all the points but I would try to give a brief idea about it.
Most likely, you would be using the host OS prompt to run the Vagrant up and Vagrant ssh command to ssh into the virtual machine.
For any task related to directory creation/ changing the permission/ changing the ownership/ running the lab validation script etc… you would be using the Vagrant prompt.
Any MongoDB related command except mongod, mongos, mongo and mongoimport (used in this course), you would be running inside the mongo shell.
Hope it helps!
Please feel free to get back to us if you have any other query.
Curriculum Services Engineer