Recently with an update to the Atom-io-editor my default file manager was changed to atom editor. This was not desired, but tolerable for bit; and I knew I’ve fixed this issue before.

I looked in the Defaut Applications of Gnome, but that looked correct and it did not have a place for the files browser.

I re-found https://wiki.archlinux.org/index.php/xdg-open which is what i was looking for. I made the following changes to the ~/.config/mimeapps.list from

Lang: 
inode/directory=atom.desktop;

to

Lang: 
inode/directory=org.gnome.files.desktop;