I run into this every time I swap branches and my xcodeproj file changes in one way or another. I have to Resolve Package Dependencies manually every time.

This is something I've been struggling with for some time. The hierarchy of my app makes this harder to diagnose. But like you, it was working fine for years. In my case, this app supported three column-layouts prior to the release of column-based split views. In order to do so, we have a concept of a NestedSplitViewController -- which is a UIViewController that owns a UISplitView. We're running into the same issue with Xcode 15 – and can't seem to pin it down.

Unfortunately the issue still persists with the changes made above. I'll file a bug via the Feedback Assistant.