src/main/resources excluded from classpath for Gradle subprojects with generated source directories #4393

Describe the bug
After updating the VS Code extension to 1.54.0, I started seeing issues with my Java application re: Liquibase. The specific error was a failur to run with Failed to configure a DataSource: 'url' attribute is not specified. but after some digging with the help of an LLM it seems that the cause was that excluding='**' was being added to the entries in .classpath/src/main/resources.

It only happened with one subproject; the agent sugested that the excluding is only added when there is a generated source dir on the build path (like build/generated/sources/dgs-codegen).

To Reproduce
The LLM created these steps and I agree that they describe my situation:

1. Open a multi-module Gradle project in VS Code with redhat.java 1.54.0
2. Ensure at least one subproject has a generated source directory on its build path (e.g. DGS codegen, annotation processing)
3. Wait for "Java: Ready"
4. Open the generated .classpath for that subproject in the JDT workspace storage (at ~/Library/Application Support/Code/User/workspaceStorage//redhat.java/jdt_ws/.metadata/.plugins/org.eclipse.core.resources/.projects//.classpath)
5. Observe that src/main/resources has excluding="**" on its entry, while a sibling subproject without generated sources does not
   The practical consequence for Spring Boot projects: the app fails to start because application.yml is not on the classpath (Tomcat defaults to port 8080, datasource properties are unresolved).

Unfrotunately I don't have a sample project to attach; mine is a closed source application.

Expected behavior
Just like in 1.53.0, src/main/resources doesn't use excluding="**", and resource files are copied to the output dir during compilation so they're available at runtime.

Screenshots
N/A

Environment

• Operating System: macOS 15.6 (Apple Silicon, arm64)
• JDK version: 17.0.18
• Visual Studio Code version: 1.116.0
• Java extension version: 1.54.0 (doesn't work) / 1.53.0 (works)

Additional Information
The excluding prop is added with both java.gradle.buildServer.enabled: "auto" and java.gradle.buildServer.enabled: "off"