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Some quick spot checks (ie picking a few random spots to look at in the manifest) , make it abundantly clear that the issue is the MD5 chunk data, which is causing the huge manifests.

I'm not sure what to do about that, it's not possible to spit it out to a downloading directory at update time because you don't know where that'll be, but there's definitely people that want it.

Maybe emitting it directly into a MD5 folder in the route dir, is the best way to handle it ? Gogrepoc itself never reads this data (and has no reason to , there's no actual point in doing offline MD5 chunk comparison when you'd need to be online to do the repairs anyway), so it'd just be a matter of writing it and deleting any outdated ones when updates are done.

Also making it optional I suppose.
Umm.. if it's temporary data, shouldn't the files be saved in a temporary folder and not in the actual installers archive?
Or maybe make it a subfolder of "!downloading"?