I opened an issue about it here: https://github.com/meteor/meteor/issues/11030
Webpack has way to deal with this, but it appears that Meteor does not (would be great if it did!).
Are the NPM modules all included at the root level of the project, or are they included by packages? I’ve noticed that meteor packages seem to keep their own version of NPM modules, even if the same version of the same module is required by the project. The “solution” I found is to clone the offending meteor package and remove it’s node deps and ensure that the project requires those instead.
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In my case it is only the app dependencies, in the node_modules of the application.