vscode-java fails to build project with pom-type dependency

I am attempting to follow https://www.graalvm.org/latest/reference-manual/python/ in VSCode, but the Java Language Support for VSCode appears to be having some difficulty. Namely, it thinks the project cannot be built, while ./gradlew build succeeds just fine.

Environment

• Operating System: macOS 13.6.1 (22G313)
• JDK version:
  openjdk 21.0.2 2024-01-16
  OpenJDK Runtime Environment Homebrew (build 21.0.2)
  OpenJDK 64-Bit Server VM Homebrew (build 21.0.2, mixed mode, sharing)
• Visual Studio Code version: 1.87.2 (Universal)
• Java extension version: v1.28.1
• Gradle 8.5

Steps To Reproduce

1. git clone https://github.com/kalaracey/graalpy-vscode-issue.git
2. Open graalpy-vscode-issue in VSCode
3. Wait for the automatic "Opening Java Projects" to finish

Java Language Server log

Current Result

VSCode's Problems tab has two problems:

• Archive for required library: '/Users/kal/.gradle/caches/modules-2/files-2.1/org.graalvm.polyglot/python-community/23.1.2/2534a71914ae30007251d1f91f67bb5b5b3431d/python-community-23.1.2.pom' in project 'app' cannot be read or is not a valid ZIP file
• The project cannot be built until build path errors are resolved

Expected Result

No problems, given that ./gradlew build succeeds.

Additional Informations

/Users/kal/.gradle/caches/modules-2/files-2.1/org.graalvm.polyglot/python-community/23.1.2/2534a71914ae30007251d1f91f67bb5b5b3431d/python-community-23.1.2.pom is the only file in its directory.

Outputs from various VSCode tasks:

• Build Server for Gradle (Build)
• Build Server for Gradle (Log)
• Gradle for Java

Start with the linked graalpy-vscode-issue reproducer and the Java Language Server, Build Server for Gradle, and Gradle for Java logs. Trace how the python-community-23.1.2.pom dependency is handled; done means opening the project in VSCode produces no build-path problems while ./gradlew build continues to succeed.