Repackage
If you edit a file in a package with external links, a REPACKAGE option should put all links that are not in the LINKS folder there.
extra; CLEAN PACKAGE should remove all files that are not used in the package.
This would avoid having to make a fresh package after every edit
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MT
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Ava MoweryCarlson commented
Hey!! It's not quite what you want, but there is something similar!
Select all the items you want to move to your existing links folder in the Link menu. Click the Hamburger menu - Utilities - Copy link(s) To... - and then simply navigate to your existing links menu.
It's not perfect as you'll still have to remember which links are which, but for me it's less annoying than constantly re-packaging the document.