In my clear desktop I booted up this morning only to find that, all apps are missing including terminal and file manager… Legit can’t do anything right now because even Firefox won’t launch…what is the best remedy to this situation if I want to retain my current configs and data?
Before you repair it would be worthwhile to make backup copies of /usr/local , /etc/ , /opt , /home , and /var once your drive is mounted. Those are directories owned by the User that Clear Linux doesn’t touch. You can read more about stateless on our website. If you have to reinstall for some reason then restoring those directories and installing the bundles you had installed should get you back to where you were.
On your mounted drive you can ls -1 /usr/share/clear/bundles to see a list of all the bundles you had installed. I’d make note of that too in case you need to reinstall.