Purge unused media files

Is there a way to purge unused media files from the media folder in one go rather than delete them all individually?

Yeah, select the first one, shift-click the last one, right-click, Move To Trash. Or just dump the whole folder. I don't think Motion minds if that folder is there or not. I'll have to check that.

If I'm understanding your question correctly, you have a motion project in a folder along with a media folder that contains a bunch of unused media?

If so:
1. Open the project
2. In the menu bar; File > Remove Unused Media
3. Save As
4. Set Collect Media to Copy to Folder in the Save As dialog
5. It shouldn't matter now as you removed the unused media, but just to be sure, uncheck Include Unused Media
6. Save

You'll now have the motion project along with just the in-use media.