There are a couple different things here - the palette manager and the flows site.
Has the flows site ever listed the nodes in your package? Looking at the code, the way you have structured things (by moving the registerType call out of your .html file) means the simple parsing done by the flow library won't find it. That isn't related to the fact you've also got plugins in there.
The package.json file includes a list of node files. Each node file can contain any number of actual nodes. Each node has a type, colour, icon etc - none of that information is in the package.json file.