In additional to Michael response, notice that the JAR is installed on the installed-plugins directory, and the information about what you did regarding to this plugin is stored on your DB (e.g If you have Service Desk installed and is running a Service Desk project with its own SLA, queue and other configurations, if you simple remove this plugin from _installed-plugins_, you won't be able to use Service Desk, but you configurations are already saved on the DB and in case if you re-install this plugin, all your configuration will be already there)
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