Resources (application.properties) automatically deleted from bin folder shortly after generation in Gradle project

Describe the bug
In a Gradle multi-module project environment, the application.properties file is correctly auto-generated/copied into the bin/main folder after a "Clean Java Language Server Workspace" command or project build. However, after approximately 5-10 seconds, the file is automatically deleted from the disk without any user interaction.
To Reproduce
Steps to reproduce the behavior:

1. Open a Gradle multi-module project in VS Code.
2. Run the command: Java: Clean Java Language Server Workspace.
3. Open the file explorer and navigate to the output directory (e.g., project/bin/main).
4. Observe that application.properties is generated.
5. Wait for about 5 seconds.
6. The file disappears from the folder automatically.

Expected behavior
The language server should copy resources from src/main/resources to the output folder and ensure they persist there for the application to use during runtime and debugging.

Environment

• Operating System: Windows 11
• JDK version: 25
• Visual Studio Code version: v1.104.0
• Java extension version: v1.54.0

Additional Information

• This issue occurs specifically in a Gradle setup where the Language Server (Eclipse JDT.LS) seems to have a conflict with the internal build/sync process.
• Attempting to set a separate output folder (e.g., bin/main/) results in a "Cannot nest output folder" error.
• The logs show a warning: WARNING: Reflective call to EquinoxBundle#getModuleClassLoader(boolean) detected.
• A temporary workaround is manually running .\gradlew.bat processResources, but the file is eventually deleted again by the language server's background synchronization.

Reproduisez le problème dans un projet Gradle multi-module Windows 11 avec Java : exécutez Clean Java Language Server Workspace, puis inspectez les journaux du serveur de langage tout en comparant le contenu généré de bin/main avec .\gradlew.bat processResources. Prenez comme point de départ le comportement signalé du dossier de sortie et de la synchronisation. Le travail est terminé lorsque application.properties reste dans le dossier de sortie après la synchronisation en arrière-plan et est disponible pour l’exécution et le débogage.