Sometimes you need to work on application code and a dependency at the same time. You might be the author of a dependency and don’t have good test coverage yet. The application can serve as an end-to-end test for the dependency. Maybe you need to debug an issue in your application and the problem seems to be in the dependency sources.

You could make changes in node_modules and manually copy the changes to the git repository of the dependency once you are done. But there is a much cleaner approach: npm link.