Discovered this along with #2441, so you can see a repro at the same repo: https://github.com/seansfkelley/node-modules-alias-loader-bug under “bonus bug”.
Summary: if you want to do local development across multiple repos and so have
npm linked them together, any loaders that accept files in
node_modules/ (such as
source-map-loader, which is explicitly intended for this purpose) must also be installed in each linked repo. This is is unexpected, sine the linked repo may not even use Webpack. It should only be necessary in the root repo, which is the one actually running Webpack.