As part of our Wikidata-Bridge work, we’ve set up a node project in a subdirectory of the Wikibase Git repository, with a package.json at client/data-bridge/package.json. As far as I can tell, LibraryUpgrader currently won’t update this project. It would be nice if it could do that.
We’re not the only ones to do this either; with code search, I can also see some nested package.json files in other projects. However, as far as I can tell only one other project would benefit from this (VisualEditor’s rebaser, cc @Esanders), so this probably shouldn’t be autodiscovered (i. e. upgrade every **/package.json) – a manually maintained list of extra package.json files would probably be enough.