When you cleaned out your root directory, did you also clean up your logs?
I have a small root partition, so have to regularly keep it clean and tidy.
For journal maintenance I use this sequence, one step at a time.
journalctl --disk -usage journalctl -r
then after visual review:
sudo journalctl --rotate sudo journalctl --vacuum-size=100M
100M is on the small side, but you can substitute a different threshold value instead.
EDIT: my original post on the subject is here: Using the Terminal Emulator in Linux Distros - #2 by zabadabadoo