Update packaged contents
To be able to PACKAGE a file and it's contents/fonts is obviously essential, however - this should not be a end to a means. Once you package you file, and then have to make changes to the file you had open (this happens a lot), the PACKAGED contents is now out of date. Could be just the .ai, or .ai and links and fonts.
Once you've PACKAGED once, there should be an UPDATE PACKAGE function. This should also be implemented in InDesign and Photoshop.
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Technically, making a new package from the original file (not the one stored within the package) is equal to updating one. It won’t overwrite an existing package, but make a new one, if I am not mistaken. Why do you think 'Update a package' would be beneficial to this existing workflow?