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It's actually hard to reproduce (so I have a little hope you'll fix it), but happens almost every week on my laptop.
The symptom is that node_modules/fs-ext/build/Release/ folder just disappears after some of "yarn install" commands. And the only thing which helps is running:
yarn remove fs-ext; yarn add fs-ext
This happens only with fs-ext (and never with some other binary extension like e.g. bcrypt). On both Node 9 and 12.
Linux, docker environment, yarn 1.19.2 (although older versions of yarn are prone too).