Nothing...The plugin alone gathers the input and acts based on its own settings.
These errors are expected, but the plugin will work just fine:
WARNING task clean-transmission Task doesn't have any input plugins, you should add (at least) one!
WARNING task clean-transmission Task does not have any filter plugins to accept entries. You need at least one to accept the entries you want.
WARNING task clean-transmission Task doesn't have any output plugins, you should add (at least) one!
On the page: http://flexget.com/wiki/Plugins/clean_transmission
disable_builtins: [details] this plugins triggers default warnings that will be shown in flexget.log. This disables those warnings.
But it doesn't actually suppress the warnings above, only lines like this:
VERBOSE details clean-transmission Task didn't produce any entries.
VERBOSE details clean-transmission Summary - Accepted: 0 (Rejected: 0 Undecided: 0 Failed: 0)