How to silence “Your disk is almost full” notification on MacOS Mojave 10.14.1 (18B75)
Put the programs on an external USB drive. They need no special write speed and you’ll be super happy once you get enough space for the OS to breathe. 

You’re right 128 GB is too small to let everything sit where it gets installed. I’d say you should have 15 GB free on the root filesystem for the best experience. 

If you’re not sure which apps are easily relocated, please post an image of your Applications folder, calculate size, sort descending so we can help point out easy apps to thin or move if you want help there.