Short answer:
For each lib in root, delete those in sub-folders to be sure.
Long answer:
There are 3 ways to use libs:
- Embedded. The lua files are loaded as part of the main addon. Out-dated!
- Bundled. The libs are in sub-folders, but have their own txt file, with the same name. Versioning is done by the ESO client.
- Stand-alone. Good for "Minion", to keep them up-to-date automatically.
The "embedded" way is the one which can break everything. The ESO client can not prevent loading duplicates, Minion does not even know they are there.