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It turns out there were several tags pointing to unreachable objects.
The trick to work around it was to modify steps 1: Instead of cloning, do a git init, then remote add, then fetch --all and fetch --tags.
Fetch will only fetch reachable objects.
https://stackoverflow.com/questions/20647495/why-is-a-cloned-repo-10x-larger-than-a-fetched-repo

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Answer selected by thorade
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