wp-cli update plugin update deployment process

Extremely happy with wp-cli so far. One issue: I can’t seem to update plugins locally, commit the changes to the remote repo and see the plugin status as updated on the remote server. This deployment process seems correct to me (git learner), but it seems to me now that updating the plugins via wp-cli or the GUI makes database changes also? This would explain why deploying changed files does not change the status of the plugin on the remote server. Is there a process in wp-cli that I am missing that updates the database after deploying plugin updates?

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