If you want to use the github plugin then you need one repo per library. (meaning you would need to create a repo called “Misc.pretty”)
This is the reason why we do no longer use it for the official library. (Basically unmaintainable)
If you want to use your current repo layout then you would need to manage git outside of kicad and point kicad to the local location of it. (This is also the only way how you can make changes to your library as kicad can only read from github via the github plugin. It can not write)