$ ./bmm -h
bmm -- a terminal application for managing bonelab mods
  -h, --help      Show help
      --token     Mod.io OAuth 2 Token
  -p, --path      Bonelab mod folder path
  -u, --update    Download subscribed mods from Mod.io, and update them if they are out of date
  -s, --subscribe Subscribe to mods that are on your disk, may not work for all mods
                  Intended for subscribing to mods gotten from fusion

You have to kinda delete all of your mods and reinstall them with bmm -u.

todo

• generate package manager db without reinstalling all mods