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install/deps: Stop flattening modules that require peer deps (#17678)

This is necessary because we don't know where their peer dep is installed.
In fact, it might not _be_ installed and that's still a valid tree.  By not
flattening it we can ensure that it's always able to load it regardless of where
it was required.

Fixes: #17639
PR-URL: https://github.com/npm/npm/pull/17678
Credit: @iarna
Reviewed-By: @zkat

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