Submodule Not Removed Completely
The submodule at "docker-livingstone" was removed from .gitmodules, but the folder still exists in the repository. Delete the folder, commit the change, then try again.
Along with all of your generated credentials and some other things, I think you must have used the Github Desktop application to clone the existing repository (https://github.com/livingstoneonline/docker-livingstone) into the same folder you had this repository checked out from.
Submodule Not Removed Completely The submodule at "docker-livingstone" was removed from .gitmodules, but the folder still exists in the repository. Delete the folder, commit the change, then try again.
Looks like you added a sub-module in this commit:
https://github.com/livingstoneonline/livingstoneonline/commit/4e39ec2a0ba6434a560e7985ccb0d38720145fb4
Along with all of your generated credentials and some other things, I think you must have used the Github Desktop application to clone the existing repository (https://github.com/livingstoneonline/docker-livingstone) into the same folder you had this repository checked out from.
I removed all the bad commits from the three branches and sent out an email for everyone on how to revert back to the working setup.