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Trunk was launching an old version of Tailwind (3.3.5, I wanted 4.0.6), so I ended up diving into the source code and found a not-exactly-documented [tools] section. [tools] and tailwindcss = "4.0.6" does the trick, and there are a few more tools with version defaults as well as some other stuff.
It would be nice to add all of these to the official website's Config page.
Also, the most recent version of Tailwind seems to be a breaking change compared to 3.x and using the default settings while expecting 4.x causes errors. Updating it would be a breaking change too, but it might be worth it to clarify the current default version (as well as for the other tools) to avoid confusion & instruct how to specify the preferred version via the config.
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