Allow extensions to handle missing node types without showing an error.

`app.js` currently identifies missing node types first, then configures the graph, then executes `loadedGraphNode` for extensions, and finally shows a dialog for missing types found in the initial list.

However, this doesn't allow extensions to port old types to new ones seamlessly. If the missing nodes was done _after_ extensions' `loadedGraphNode` was run on the configured graph, it would be much more representative of the current state. (or, extensions' `loadedGraphNode` could be fed the missing node types lists, and remove types it properly handled).