Resources (application.properties) automatically deleted from bin folder shortly after generation in Gradle project #4398

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.