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Maybe I'm not reading this correctly. It looks like the function returns True if it finds any .c or .h file that contains the string '[clinic input]'. It doesn't seem to only check files that have changed.
I was considering adding a checkum for the *input* to the third comment (what I call the "output line"). That would let this checker compute the checksum for the input and output sections and confirm that they match. If the input had changed, the checksum would fail, and you'd know they hadn't run clinic recently.