What happened to the class PatchReader.java that was in app.jar for IJ 2024.1, but not IJ 2024.3.5?

Your memory is correct!

Per the docs:

2024.2+
Requires IntelliJ Platform Gradle Plugin (2.x)

ref

A good first step would be to complete the migration to 2.x plugin (latest version is 2.5.0 as of writing), and then trying what is advised above again.