It's possible that you won't be able to unless you do it manually. Also, depending on the plug-in and what's it's designed to do you might not want to. For example if the plug-in is for effects those effects will not display in the absence of the plug-in..... if they were used in the file.
Alternatively, if the plug-in was for, say, an asset management system that was used in a prior incarnation of the file it might not be a problem. Some asset management systems like to keep itself hooked to a file (so to speak) even once they have severed ties (again, so to speak).
Bottom line, in my opinion.... and I'm sure others will have other input, it depends on the plug-in. It's likely that you either won't want to package (because output will be incorrect) or you'll need to do it manually.
Can you give more info as to the nature of the file? Did you create it? Did you get it from a client? What plug-in is missing? Why do you need to package it and for who?
~Soilworker
