If a player's permission set changes, update the player's permissions.

eg. If a player is no longer allowed to vanish, unvanish the player.

Where did I say it did that for all permissions?
Sure, I should have been more specific about what permissions I meant, but for the toggle permissions, this was true and correct, and my understanding of the code was not at all wrong?

Anyway, moot point, fixed/extended/remedied now, sort of, with the onJoin hook at least.

Heh, I would settle for VanishNoPacket actually checking permissions when a command is issued.
As it stands now, it checks all the permissions on startup, and if they change while the server is running, that change is ignored.

You have no less than TWO join hooks. Perhaps one of them can refresh the permissions, if you don't want to check the permissions when actually needed?

Only toggle-based permissions are stored in any way. Please read over the code before commenting on the code. :/

Closing 4.0 issues, I'd rather not have scattered planning for the future which may or may not come to pass