class file in source root directory interferes with package explorer

I have a Maven project with the usual structure. When for some reason any `*.class` file is present in the `src/main/java` root directory, the Package Explorer shows an empty source directory without subpackages/classes and no expansion option.

Additionally when the class file is empty, the Error Log view infos:
```
Could not index empty /project/src/main/java/x.class
```

# Versions

* Eclipse IDE for RCP and RAP Developers
Version: 2026-06 (4.40.0)
Build id: 20260604-0653

* openjdk version "21.0.12.1" 2026-08-18 LTS
OpenJDK Runtime Environment Temurin-21.0.12.1+1 (build 21.0.12.1+1-LTS)

Reproduce this in a Maven project by placing a valid or empty *.class file in the src/main/java root directory. Start with the Package Explorer behavior and the Error Log message, then trace the relevant indexing or source-folder handling; done means packages and classes remain expandable and an empty class file does not break the explorer.

Written by the indexing model from the issue text.