They set out to reduce build times, not to reduce git checkout times. It turns out that 99% of the entire build was spent downloading code.
If the title is a lie (which it probably is), then nevermind that number, but it's clear where it came from.
The only way build time could have been reduced by 99% is if every part of the build other than cloning is negligible. It is far more plausible to assume that the title is simply wrong.
Presumably the build does more than just clone
Where in the article does it say that? The article says this:
> This simple one line change reduced our clone times by 99% and significantly reduced our build times as a result. Cloning our largest repo, Pinboard went from 40 minutes to 30 seconds.
Both of those sentences say the clone time was reduced by 99%. There are percentage numbers given for how much the build time was reduced, nor any numbers about the total build time.