`Refresh using native hooks or polling` causing rebuilds for changes in java output folders

Let's make sure issue is not already fixed in latest builds first.

- [x] I verified I can reproduce this issue against [latest Integration Build of Eclipse SDK](https://download.eclipse.org/eclipse/downloads/)

## Steps to reproduce

From a fresh installation and clean workspace:

* Check the `Refresh using native hooks or polling` workspace setting
* Create a large Java project containing many programs, that will take several seconds to build.
* Do a clean
* Add a text file into the `/bin` of the java project
* Watch Eclipse try to rebuild the java project

I tried

* Unchecking `Refresh using native hooks or polling` solves the problems.

I expected: *Changes within Java output directories to be ignored, as per project settings*

But got: *Changes in Java output folders, with this setting on causes rebuilds. And for larger java projects, while a build is happening, the next poll kicks in because its been updating `/bin`, stops the current build and starts another, causing a build loop.*

## Here is some relevant log output

N/A

## Tested under this environment:
* OS & version: Windows 10
* Eclipse IDE/Platform version (as shown in *Help > About*): 4.23, and tested on 2023-12

## Community

- [x] I understand reporting an issue to this OSS project does not mandate anyone to fix it. Other contributors may consider the issue, or not, at their own convenience. The most efficient way to get it fixed is that I fix it myself and contribute it back as a good quality patch to the project.