1) Easily fixed:
https://github.com/kovidgoyal/calibr...8bff364d981ac3
2) Personally, I like to keep the links, as people that read them on devices with useful browsers might like to click them once in a while, plus it is good for the NYT to get visits.
3) No idea why that might be -- I never used the old recipe, so it's hard to say what's different.