[Java] Do not publish modules based on filenames

### Describe the bug, including details regarding any error messages, version, and platform.

Arrow Java should not publish modules based on filenames. Flatbuffers/Protobuf can probably be shaded to avoid this. We can potentially remove usage of jsr305 in favor of another library.

```
[WARNING] * Required filename-based automodules detected: [flatbuffers-java-24.3.25.jar, jsr305-3.0.2.jar, protobuf-java-3.25.1.jar, protobuf-java-util-3.25.1.jar]. Please don't publish this project to a public artifact repository! *
```

- [x] https://github.com/apache/arrow/issues/43396
- [x] https://github.com/apache/arrow/issues/43437
- [x] https://github.com/google/flatbuffers/issues/8348

### Component(s)

Java

まず Java の公開設定と、flatbuffers、protobuf、jsr305 が公開される成果物にどのように含まれるかを調査します。プロジェクトの build または公開コマンドで filename-based automodule warning を再現します。公開されたモジュールが filename-based automatic modules に依存しなくなり、必要な機能を維持できれば完了です。

索引モデルが issue の本文から書いたものです。