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I have configured Git to use a specific CA certificate, but how can opt-out for it other than using the switch -c http.sslVerify=false? (or enforce other certificate which seems better in terms of security).

Okay, a workaround was to create a shell script for a shortcut and use it like

gitf clone

That is okay for a quick test in a secured and trusted environment but it is a potential security breach. Do not try this at home.

The real gotcha comes then in if I would like to use the Atom editor. Somehow I cannot find an option for the git executable.

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You'd better add this CA to a bundle of valid CA and keep using it for all cases with

git config --add --global http.sslcainfo=/path/to/cabundle
git config --add --global http.sslbackend=openssl

Using https://curl.haxx.se/docs/caextract.html as starting CA bundle sounds a good idea in my opinion.

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