The LuckPerms Developer API is changing a lot. My suggestion is to make the methods backward compatible, so you don't remove the methods, and instead add a message in the console, like:

[LuckPerms] The plugin MagiChat is using the method me.lucko.luckperms.api.Group.getAllNodes was removed in newer versions of LuckPerms. Please report it to the plugin author.

That would plugins to not break on every LP update 😄

"The LuckPerms Developer API is changing a lot" - Are you kidding me? There has been one backwards compatible change since it was first released.

I also documented this change very clearly, and gave specific wanting about which methods were removed.
https://www.spigotmc.org/resources/luckperms-an-advanced-permissions-plugin.28140/update?update=145645
https://gist.github.com/lucko/fdf6ae4b2d9e466d8103dd9c68e5db9e
https://github.com/lucko/LuckPerms/wiki/Developer-API#versioning

I suggest you read up on Semantic Versioning. LuckPerms follows it.
http://semver.org/

The version bumping to 3.0.0 is enough to tell you there were backwards incompatible changes in that release.

"That would plugins to not break on every LP update 😄"
........ seriously? One update.