The creds files are an artifact with secrets, the others are the actual config, and the state of the config for the user. Pub/sub permissions, etc.
Depending on your strategy, you can choose to throw them away or not If you ever need to revoke, you'll need the user public key, unless you want to revoke at a higher level (ie all JWTs issued since some day or all JWTs issued by a signing key). You can absolutely try to import a creds to recover the user.
In Git you should store all the JWTs for operator and accounts at a minimum. If you use bearer user JWTs treat those as secrets as well since they don't require an NKEY to authenticate.
In the end, what you preserve is a matter of what you'll need to restore your environment. With the new state of the arts (latest server versions) it is possible to create an auth callout, and simply generate user NATS credentials whenever the user connect by inspecting other data that the user provides (token, username, IP, etc). This means that code is used to on-board the user and generate permissions for that user on every connect.