To be honest I can't remember which one it is, think it's quite an old one that I used to use for an old googlecode repo about 3-4 years ago. You can download it or open the file and copy the contents if you want.
The reason you need the addon.xml files extracted is so that the generator can search through the folders and extract the information from each file (it searches through every sub-folder in the directory the generator is located at). This information is used to build the addons.xml - this is the file that lists all the add-ons and is the file Kodi checks against to see what you have on the repo. The zips are required as that's what Kodi downloads and then it shoves the zips in the packages folder on your system and extracts them and installs any dependencies needed.
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I use the generator that creates the zips too.
You don't need to move anything, just run it from the top level(root) of your repo and it creates everything for you.
The only thing it fails to do (if yours is the same script) is add the version number to the end of the changelog file.
I just edit the filename from changelog.txt to changelog-x.x.x.txt after the script has finished.
I've never got round to fixing that. lol