fix(nm): Reinstall removed module directories

[larixer]

What's the problem this PR addresses?

When you remove unplugged directory with pnp linker, it reinstalls the directory again. This behaviour is currently different for the nm linker, it will perform reinstall only when top-level nm folder is removed. The PR changes this for the nm linker, so that both linkers behave the same - when you remove directory deep inside node_modules the nm linker reinstalls only this directory and rebuilds the module if needed. The same logic applies to the bin symlinks - removed bin symlinks gets recreated by the nm linker.

Closes #3214

How did you fix it?

I use the fact that the nm linker writes node_modules/.yarn-state.yml as the last operation of the link step, hence it must have the mtime which is greater than all the files and folders inside node_modules. To detect whether the user has removed any module directory inside node_modules, it is enough to check whether each parent node_modules folder has mtime >= state_file_mtime and if it does - the user has modified the directory, we then perform readdir and find entries deleted by the user, if any, and record these modifications in the preinstall state. The algorithm that diffs install and preinstall state later does the rest of the job of reinstall deleted modules and directories.

Checklist

• I have read the Contributing Guide.

• I have set the packages that need to be released for my changes to be effective.

• I will check that all automated PR checks pass before the PR gets reviewed.

[penx]

@arcanis @merceyz is there anything that can be done to get this in? 🙏