So the long install works (copy pasting in code by hand) but the patch install using the ROM site introduces typos and bugs that destroy certain syntax markers. I don't have much else to suggest because I'm not too familiar with twine tools myself but I'll be on the lookout for patching methods that'll make things easier
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That's odd, because the patcher definitely works for me (just tried it again in case I was going crazy). Just to make sure, you're definitely using the patcher on an unmodified version of the index file you get from the game's official download - FTAG 064a.zip from the Downloads section of the page?
Though yeah, if you find a better way - ideally something that can handle multiple mod installs while not requiring the user to download any programs - do let me know :3