Applying with GradleUp's Shadow forces local Gradle API on `compileOnly` configuration

### Expected Behavior

The local Gradle API (`DependencyHandler#gradleApi()` should not be used under the presence of the internal flag `org.gradle.unsafe.suppress-gradle-api`.

### Current Behavior

Attempting to suppress the usage of the local Gradle API while applying *both* the Plugin Publish and Shadow plugins will result in the local Gradle API being used anyway.

This is also a bug with the Shadow plugin (see GradleUp/shadow#1422), but it also needs to be fixed with this plugin (see bottom of the issue for my proposed change).

### Context

Part of what the Plugin Publish plugin does to work with the Shadow plugin is remove the Gradle API from the `api` configuration and add it to the `compileOnly` configuration. This is fine and has worked for a while now, but with the ongoing work on publishing external Gradle APIs (gradle/gradle#29483), this will pose problems when trying to use a non-local Gradle API.

Additionally, the Shadow plugin already does this (see [ShadowJavaPlugin#Project.configureJavaGradlePlugin](https://github.com/GradleUp/shadow/blob/5e44c138592c37b5b01a3bbd23cc7ad468f5297e/src/main/kotlin/com/github/jengelman/gradle/plugins/shadow/ShadowJavaPlugin.kt#L101-L114)) when the `java-gradle-plugin` plugin is applied -- a plugin which this plugin applies.

### Steps to Reproduce

1. Generate a plugin project using `gradle init`
- When I reproduce this bug, I used the Groovy preset and the Groovy DSL. But this bug should be present on whatever language or DSL you use.
2. Add the following to your `gradle.properties` file:
```properties
systemProp.org.gradle.unsafe.suppress-gradle-api=true
```
3. Apply `com.gradle.plugin-publish` to your project.
4. Apply `com.gradleup.shadow` to your project (latest as of writing is `9.0.0-beta13`)
5. Run the `dependencies` task for your project, and see that the local Gradle API (marked as "unspecified") continues to exist in the `compileOnly` configuration.

For now, I am working around this by putting this in my `build.gradle` script:
```gradle
afterEvaluate { project ->
project.configurations.named(JavaPlugin.COMPILE_ONLY_CONFIGURATION_NAME) { compileOnly ->
compileOnly.dependencies.remove project.dependencies.gradleApi()
}
}
```

### Your Environment

Gradle 8.14
Gradle Publish Plugin 1.3.1
GradleUp Shadow 9.0.0-beta13

### Proposed Fix

Since the sources for this plugin are available as part of the Plugin Portal, I saw where this is taking place and would like to offer a quick fix for this.

In `PublishTaskShadowAction.java:52`, method `#manipulateDependencies`

```java
private void manipulateDependencies(ConfigurationContainer configurations) {
Dependency gradleApi = project.getDependencies().gradleApi();

Configuration api = configurations.findByName("api");
if (api != null) {
api.getDependencies().remove(gradleApi);
}

Configuration compileOnly = configurations.findByName("compileOnly");
if (compileOnly != null) {
compileOnly.getDependencies().add(gradleApi);
}
}
```

This can be changed to look something like this:

```java
private void manipulateDependencies(ConfigurationContainer configurations) {
Dependency gradleApi = project.getDependencies().gradleApi();

Configuration api = configurations.findByName("api");
if (api != null && api.getDependencies().remove(gradleApi)) {
Configuration compileOnly = configurations.findByName("compileOnly");
if (compileOnly != null) {
compileOnly.getDependencies().add(gradleApi);
}
}
}
```

In this implementation, there will still be an attempt to remove the local Gradle API from the `api` configuration like usual. If the remove was successful (it was present), *then* continue with adding it to the `compileOnly` configuration.

Start at PublishTaskShadowAction.java:52 and inspect manipulateDependencies, then reproduce with Gradle 8.14, Plugin Publish 1.3.1, Shadow 9.0.0-beta13, and org.gradle.unsafe.suppress-gradle-api=true. Run the project's dependencies task to verify that the local Gradle API is no longer present in compileOnly when it was not removed from api.

Written by the indexing model from the issue text.