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troubleshooting
The node.js module resolving algorithm is pretty simple: module dependencies are looked up in node_modules folders in every parent directory of the requiring module. When you npm link modules with peer dependencies that are not in your root directory, modules can no longer be found. (You propably want to consider peerDependencies with npm link as broken by design in node.js.) Note that a dependency to the application (even if this is not the perfect design) is also a kind of peerDependency even if it's not listed as such in the module's package.json.
But you can easily workaround that in webpack: Add the node_modules folder of your application to the resolve paths. There are two config options for this: resolve.fallback and resolveLoader.fallback.
Here is a config example:
module.exports = {
resolve: { fallback: path.join(__dirname, "node_modules") },
resolveLoader: { fallback: path.join(__dirname, "node_modules") }
};