Remove lines from .gitroot/plugins.yml and GitRoot will delete the plugin. Be carrefull when doing that GitRoot will not update .gitroot/plugins.yml of sub-repo which could use it.
1- - url: "file:///plugins/ladybug/ladybug-0.0.1.wasm"
2- crc32: null
3- name: ladybug
Commit your change and push git add . && git commit -m "delete plugin ladybug" && git push. When the change will be in the defaultBranch nobody on your instance will be able to use it anymore.
You need to tell to your users that the plugin no longer exist.