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The command line tool and the plugin are always version-matched. Setup installs the plugin from the tool itself, so the two never drift apart. Updating one updates the other.
nito update upgrades the nito binary through the package manager you installed it with, then re-syncs the plugin so the two stay version-matched. If you prefer, you can upgrade the binary directly and let the next command re-sync the plugin:

Doctor and Update

Health checks and the full update and repair flow.

Uninstall

Remove the plugin, sign out, and remove the tool.