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Here's an issue I've experienced with using upgrade: https://github.com/yarnpkg/yarn/issues/5749

> and I noticed that certain packages were completely missing from the node_modules folder, yet are listed in yarn.lock

Sounds like what I'd expect from running yarn clean...

(If anyone isn't aware: that command doesn't clean target folders but rather goes crazy inside node_modules.)

Yeah you're misreading my issue