Yup this is a limitation of the "transactional commit" feature : It's hard for me to identify a "transaction" when it comes from the SYSTEM (that is, automated modification made by jenkins, in the background).

I think it should be better handled during a "human" modification (because in that case, 1 http request = 1 scm transaction).
I don't know if you can modify multiple module configurations during 1 http request (I don't have multimodules on my current instance), but if you can, I think there will only be 1 commit.

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