A quick and dirty approach that will usually work. You could copy your original file, and then in the copy make a tiddler $:/kill
<$button>SCRUB
<$action-deletetiddler $filter="[all[tiddlers]!is[system]]"/>
</$button>
Be sure to close this tiddler so that it's title is $:/kill and not "New tiddler ..." or "Draft of ...".
Press the button and all non-shadow tiddlers that are not system tiddlers will be deleted.
Your plugins are usually shadows, and so won't be deleted.
Your configuration are usually system tiddlers, and so won't be deleted.
BUT, you may have excess system tiddlers that aren't for configuration that will be retained. And if you have any required additional macros that were not shadows and not system then they will be zapped.
Good luck,
Mark