Shattenjaeger wrote "it doesn't sound like there are any .mpk builder apps in the wild, so how do the rest of you do it?"
After an update, i copy, then unpack core.cpk using 7zip to the backupfolder in my archive
(7zip can unpack pretty much anything, as long as the file is structured as a (by 7zip) supported packed file,
regardless of the file-extension).
Then i copy over those files i want to change to the folder of my current modversionfolder, edit them and
use method #2, creating a zip-file which i then duplicate, rename to .mpk and copy to the mod-folder of the game.
The problem with mehod #1 is that you end up with an additional folder in the archives structure, which the game
then cannot process, because it does not fit anymore into the virtual filesystem as it should.
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There is also a third option, in which you open the packed file with a compression program that includes a basic filemanager,
delete everything you do not need, change the file you want to change in an external editor,
then save (preferrably to a new location) and close the archive again.
Instead of directly editing the file within the archive, you can also keep the compressionprograms filemanager open,
edit the file externally, save it, then drag and drop it into the place in the filestructure of the archive,
then save (preferrably to a new location) and close the archive again.
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Small correction

"Select the header.xml, content folder, and data folder and right-click them. Then rename it to mpk." should be something like
"Select the header.xml, content folder, and data folder and right-click them to pack them, then rename the created archive to mpk."