Type Hierarchy is sometimes not complete in recent versions

I've hesitated to raise this issue for over a year now because I can't find a succinct way to demonstrate it outside of a large project that I cannot share.

The issue has arisen somewhere after version 2024-09 and is still present in 2025-12. My project is many thousands of classes and for quite a few of them the type hierarchy (the one accessible by F4) is incomplete. For example I have a `public class BaseApi {..}` and several subclasses of it, but the full hierarchy is shown as simply `Object -> BaseApi`. Under 2024-09 the full hierarchy is correctly shown, which is 4 additional classes:
```
- Object
- BaseApi
- AdminApi
- UserApi
- etc..
```
Some classes work correctly and I get the correct full tree. I have not been able to spot a pattern. It does not seem to matter if it is a `class` or `interface`, I get a mixture of results either way.

I can still find all subclasses using References -> Workspace.

The problem doesn't seem to happen in any of my other projects, all of which are significantly smaller. It seems to be confined to this particular behemoth.

I have tried recreating the workspace from scratch with just this one project in it, but no luck. Colleagues working on the same codebase have exactly the same problem unless they also downgrade to 2024-09. I am on Windows, two of them are operating on Macs. I've tried this with Java 21, 23 and 25 over the last year or so, too. I am not using any additional plugins, I download the `.zip` from the Eclipse download page, unzip it and execute. This problem is immediately evident.

Basically every time I migrate to a different PC or need to reinstall I try the latest version of Eclipse but normally give up and go back to 2024-09 since I know it works. Personally I make heavy use of the Type Hierarchy view to navigate around my codebase. I would like to upgrade to the latest version since 2024 is falling pretty far behind now. Also I've recently bought a 4K monitor and 2024-09 doesn't play nicely with it :(

There's an oooold bug https://bugs.eclipse.org/bugs/show_bug.cgi?id=577069 which sounds very similar, but it also sounds like it's been solved, and in any case I am seeing the problem in a much later release.

I don't really know how to investigate this problem further. Any suggestions?