Open Project Bay and turn of the option to automatically retain media when removed from the project. Also do this for your default project (if you use one) and save it to ensure it's the case for all future projects.
If you want to archive your finished project:
Glue/bounce/'trim to active take' for all your tracks to get rid of unused take references and trimmed media. Save as a new file in a new directory and while doing this check the option to move the media. Now you can delete the old folder and it's contents (nothing there is referenced by the final version).
Keep in mind that some plugins may reference files outside the project folder and Reaper cannot know about this. In this case, what I said above isn't true; there may still be file references from e.g. samplers.
Basically the bad news is that you always have to do stuff like this carefully and manually because there are many variables, which is why it's not easy to automate.
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