Lots of applications refuse to start (VLC, SSR, Graphical software management Network manager...)

Please read this:

Please boot a Manjaro USB stick and execute as root:

fsck /dev/sdc1
fsck /dev/sdc2
fsck /dev/sda1
fsck /dev/sda2

When you encounter an error, look up the exact error message on your phone / another computer and fix it.

Once done, shut down, remove the USB stick and boot normally

Perform the xdg-open again on the same file. If that works flawlessly, try your other applications too.