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Supposedly, using --no-package-lock option should prevent this behavior, but it made no difference when I tried it just now. However, even if it did, the overall developer experience would still be poor. Consider the use case of using yarn and tracking yarn.lock instead of package-lock.json (having multiple/competing lock files is not recommended). AFAICT, yarn has no --no-save equivalent so it seems reasonable that a developer might use npm install --no-save [--no-package-lock] some-package to temporarily install a module for experimentation. As others have noted, it is quite surprising to find that doing a one-off installation of a module should remove anything, especially things that are almost completely unrelated (that is, aside from happening to be part of the same project).
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