`gazelle:python_manifest_file_name` not applied in subdirectories

# 🐞 bug report

### Affected Rule

[`gazelle`](https://github.com/bazel-contrib/rules_python/blob/main/examples/bzlmod_build_file_generation/BUILD.bazel#L90-L93) with `gazelle = "@rules_python_gazelle_plugin//python:gazelle_binary"`.

### Is this a regression?

I don't think so.

### Description

[Gazelle documentation](https://github.com/bazel-contrib/bazel-gazelle?tab=readme-ov-file#directives) describes directives as:
> Directives apply in the directory where they are set and in subdirectories. This means, for example, if you set # gazelle:prefix in the build file in your project's root directory, it affects your whole project. If you set it in a subdirectory, it only affects rules in that subtree.

Thus, I expected [`gazelle:python_manifest_file_name`](https://github.com/bazel-contrib/rules_python/blob/main/gazelle/README.md#directives) directive to apply to targets within the subfolders. I don't think this is the case, however. It seems like gazelle only considers directives at the root BUILD file.

## 🔬 Minimal Reproduction

See https://github.com/bazel-contrib/rules_python/compare/main...hartikainen:gazelle-hub-change. Running this gives me:

Given the directives in [`jax/BUILD.bazel`](https://github.com/bazel-contrib/rules_python/compare/main...hartikainen:gazelle-hub-change#diff-f767eeff89c3e51bca27e7684abee92f362583542d781aac5a378c614e3bb7a0R3-R4) and [`numpy/BUILD.bazel`](https://github.com/bazel-contrib/rules_python/compare/main...hartikainen:gazelle-hub-change#diff-adcf17f9e663d83e26a6efe5842cdfd69bf37f1827d99fe4674f9d583c754258R3-R4), I would expect both `py_binary` targets to have the right `deps` (as I have manually written them) after running `bazel run //:gazelle`. Unfortunately, gazelle does not recognize the directives in the subdirectories and fails.

## 🔥 Exception or Error

Details

```console
$ bazel run //:gazelle
INFO: Analyzed target //:gazelle (0 packages loaded, 2 targets configured).
INFO: Found 1 target...
Target //:gazelle up-to-date:
bazel-bin/gazelle-runner.bash
bazel-bin/gazelle
INFO: Elapsed time: 0.162s, Critical Path: 0.00s
INFO: 1 process: 6 action cache hit, 1 internal.
INFO: Build completed successfully, 1 total action
INFO: Running command line: bazel-bin/gazelle
gazelle: ERROR: failed to validate dependencies for target "//jax:main":

"jax/main.py", line 5: "absl.app" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py absl.app TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore absl.app' in the Python file.

"jax/main.py", line 5: "absl" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py absl TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore absl' in the Python file.

gazelle: ERROR: failed to validate dependencies for target "//jax:main":

"jax/main.py", line 6: "absl.logging" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py absl.logging TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore absl.logging' in the Python file.

"jax/main.py", line 6: "absl" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py absl TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore absl' in the Python file.

gazelle: ERROR: failed to validate dependencies for target "//jax:main":

"jax/main.py", line 7: "etils.eapp" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py etils.eapp TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore etils.eapp' in the Python file.

"jax/main.py", line 7: "etils" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py etils TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore etils' in the Python file.

gazelle: ERROR: failed to validate dependencies for target "//jax:main":

"jax/main.py", line 8: "etils.epath" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py etils.epath TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore etils.epath' in the Python file.

"jax/main.py", line 8: "etils" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py etils TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore etils' in the Python file.

gazelle: ERROR: failed to validate dependencies for target "//jax:main":

"jax/main.py", line 9: "jax.numpy" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py jax.numpy TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore jax.numpy' in the Python file.

"jax/main.py", line 9: "jax" is an invalid dependency: possible solutions:
1. Add it as a dependency in the requirements.txt file.
2. Use the '# gazelle:resolve py jax TARGET_LABEL' BUILD file directive to resolve to a known dependency.
3. Ignore it with a comment '# gazelle:ignore jax' in the Python file.
```

## 🌍 Your Environment

**Operating System:**

  

macos Sequoia 15.5 (24F74)

  

**Output of `bazel version`:**

  

bazel version

Bazelisk version: 1.26.0

Build label: 8.3.1

Build target: @@//src/main/java/com/google/devtools/build/lib/bazel:BazelServer

Build time: Mon Jun 30 16:26:17 2025 (1751300777)

Build timestamp: 1751300777

Build timestamp as int: 1751300777

  

**Rules_python version:**

https://github.com/bazel-contrib/rules_python/commit/39703fa18135fae3bcc458490a0b8266ca85e513

**Anything else relevant?**

N/A

Start with the linked minimal reproduction, especially the directives in jax/BUILD.bazel and numpy/BUILD.bazel, then run bazel run //:gazelle to reproduce the dependency errors. Done means python_manifest_file_name directives in subdirectories are applied to their targets and the generated dependencies validate without these errors.

Written by the indexing model from the issue text.