Bazel incorrectly caches resources of java_plugins

### Description of the bug:

I have a Java annotation processor defined in a `java_plugin` with some JSON file `resources`. This generator is applied to a datamodel `java_library` and generates a `.java` file based on the JSON file if the `java_library` contains a certain annotation.

After I edit the JSON file, a subsequent `bazel build` does not generate Java source files using the updated version of the file - it instead uses a cached old version. This is most apparent when there is a compile error as a result of the original JSON file, and a subsequent change to the file does not lead to the error going away.

### Which category does this issue belong to?

Core, Java Rules

### What's the simplest, easiest way to reproduce this bug? Please provide a minimal example if possible.

Please see minimal example repository here: https://github.com/SimplyTheOther/Bazel-bug-replication

1. Execute `bazel build //datamodel:station-datamodel`
2. Note that compilation fails, saying `error: cannot find symbol @FakeAttr public class S3Parameter {}`
3. Delete the line saying `@FakeAttr` from `datamodel/src/main/resources/generator/model/S3Parameter.json`
4. Execute `bazel build //datamodel:station-datamodel`
5. Note that compilation fails with the same error
6. Execute `bazel clean`
7. Execute `bazel build //datamodel:station-datamodel`
8. Note that compilation succeeds and that the generated `S3Parameter.java` file does not contain any reference to `@FakeAttr`

You can also repeat in the opposite direction, i.e. going from an `S3Parameter.json` that contains no `@FakeAttr`, and seeing that it erroneously continues to compile when the line is added.

### Which operating system are you running Bazel on?

Linux (also replicated on macOS)

### What is the output of `bazel info release`?

release 8.0.0

### If `bazel info release` returns `development version` or `(@non-git)`, tell us how you built Bazel.

_No response_

### What's the output of `git remote get-url origin; git rev-parse HEAD` ?

```text
https://github.com/SimplyTheOther/Bazel-bug-replication.git
314789ab0a50cbe870d6499c5517fe39b2a27b76
```
```

### If this is a regression, please try to identify the Bazel commit where the bug was introduced with bazelisk --bisect.

_No response_

### Have you found anything relevant by searching the web?

No

### Any other information, logs, or outputs that you want to share?

_No response_

Reproduce the failure with `bazel build //datamodel:station-datamodel` using the linked minimal repository, editing `datamodel/src/main/resources/generator/model/S3Parameter.json` between builds. Trace how the `java_plugin` resource reaches generation and cache invalidation, then verify that changing the JSON causes `S3Parameter.java` to be regenerated without `bazel clean` and that both annotation directions compile correctly.

Written by the indexing model from the issue text.