The problem is that our system doesn't know which .jar file is which plugin.
Can't you make like a thing to show a page with all plugins and a small button like a recycle bin, and just take every *.jar file from the /plugins directory and show them on that page without the .jar extension? And when for example user deletes the plugin "Essentials" it will remove the configuration folder too. (Not trying to be bad, only a suggestion, sorry if it's too direct 
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