I think it might confuse readers if there's a file that's just called "LICENSE" in the root folder that contains the MIT license, but some of the contents within the repo are under GPL-3. Would it make sense to keep the filename as "LICENSE-MIT" to call out that this is a specific one, not comprehensive of all contents?

I think it might confuse readers if there's a file that's just called "LICENSE" in the root folder that contains the MIT license, but some of the contents within the repo are under GPL-3. Would it make sense to keep the filename as "LICENSE-MIT" to call out that this is a specific one, not comprehensive of all contents?

Yeah I can see that. Typically the extensions are only used when there are multiple licenses with the same name in the same folder. In this case we have COPYING (GPLv3) and LICENSE (MIT), and the README lists the licenses at the top and we dive into the coverage at the bottom. We should be good here, and this was the original recommendation from legal, but let me know if you feel strongly (I don't).