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I have to admit, this is probably a quite uncommon use case, but still wanted to report it because maybe it can be fixed easily.
This is based on the same example as #37. Rename your node_modules directory and symlink it:
mv node_modules .node_modules_develop
ln -s .node_modules_develop node_modules
Then extract the typings. You will get a huge definitions file with a lot of inlined types. It seems like the symlink is confusing the logic that figures out how to deal with a dependency.
I've been using the symlink for a long time now as a technique to make it easy and fast to switch between the modules required for my develop and release branches. It hasn't caused any problems with NPM itself or other tools so far.