Is there a system for sorting graphics that are active in an Indesign document?

If you want to include links that are on the pasteboard, use the copy links utility because File>Package won't collect them. If you want to determine which links are not used, you can change the label color of the copied links (on a Mac, the label color is under File), then copy the labeled links into the original links folder, selecting the replace option. The links without a label color are not used. you can sort the files view by label color.

I would recommend to package the whole InDesign file with all assets.

• File > Package …

Or if you work with INDB files, in the book panel menu:

• Package for print …

There is a utility in the Links panel menu which may be useful. It's called Copy Links To. It lets you gather all the links in a particular file and copy them to another folder. (Then you could discard the old folder that contained unused graphics.)

This article describes the feature:

https://indesignsecrets.com/gather-links-without-packaging.php