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This issue is very similar to what happens to me. You will see in OpenBSD the "diff" command that comes with it does not have the "--rcs" "--strip-trailing-cr" options and therefore fails with the same error code.
One way I see to solve this issue is to create a defcustom in which we can define the correct diff binary command (in my case gdiff, from GNU Coreutils, in the case of Windows to the correct diff binary).
In this link there is an idea of how this change would be implemented.
Right, that makes sense. I'll have the default value be gdiff if available, diff otherwise. And the user can customize. On the first invocation, it will check to verify that the necessary options are supported, and report a better error if they aren't.
Apheleia gives exits with exit code 2 on Windows 11 with doom emacs:
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