The project editor, who is a separate person from the copyeditor. The copyeditor flags, I respond, then the project editor reads both and makes the call. The acquisitions editor is over her, so if I really dug my heels in over something then in theory it would go up to him for arbitration. But at the end of the day, the publishing company as a whole is the boss. They bought it from me and it's theirs to do with as they please. I should probably just trust that the project editor knows what she's doing and will make the common sense call on everything.
Side note: When I want to protest a flag, the convention is for me to type STET immediately following it. This morning, I commented on something unrelated with an ironic "I'm hilarious!" and Mr. Clod immediately responded, "Stet."
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