Today, on two occasions, I uploaded sites from scratch, where I had completely deleted the files on the server.
What I noticed is that everything got uploaded just fine EXCEPT my “cms” folder. Neither site uploaded its CMS folders.
I then did a local download of the sites, and these folders downloaded correctly. Not sure what is going on here, as I have never seen this before.
To fix it, I synced the LOCAL folder to the SERVER, which copied up the missing CMS folders.