Fix Gradle metadata repository service scoping

[jormundur00]

Fixes #415

What changed

This PR fixes multi-module Gradle builds where different subprojects configure different reachability metadata repositories.

Before this change, Native Build Tools could reuse repository settings from the first subproject that initialized the shared metadata service. That meant later subprojects could silently use the wrong metadata repository.

After this change, each subproject uses its own configured metadata repository.

Why

Multi-project builds can now safely use different metadata repositories per subproject without cross-project leakage.

Example

Before:

project(":app1") {
    graalvmNative {
        metadataRepository {
            uri = uri("file:///tmp/metadata-repo-a")
        }
    }
}

project(":app2") {
    graalvmNative {
        metadataRepository {
            uri = uri("file:///tmp/metadata-repo-b")
        }
    }
}

In some builds, app2 could still end up using the repository configuration from app1.

After:

app1 uses metadata-repo-a and app2 uses metadata-repo-b, matching each subproject's own configuration.

Implementation summary

• Scope the shared Gradle metadata service per subproject so one project's repository settings do not leak into another.
• Keep service reuse within a single project while allowing different subprojects to carry different metadata repository parameters.
• Add a multi-project regression that verifies each subproject resolves metadata from its own configured repository.

Validation

Run from the issue worktree with JAVA_HOME and GRAALVM_HOME set to the installed GraalVM 17 runtime:

• ./gradlew :native-gradle-plugin:functionalTest --tests "org.graalvm.buildtools.gradle.NativeConfigRepoFunctionalTest.subprojects can use different metadata repositories" passed.
• ./gradlew :native-gradle-plugin:test :native-gradle-plugin:inspections passed.
• ./gradlew :native-gradle-plugin:configCacheFunctionalTest --tests "org.graalvm.buildtools.gradle.NativeConfigRepoFunctionalTest.subprojects can use different metadata repositories" passed.
• grund fmt . --marker --check passed.
• Targeted grounding checks resolved and found the changed FS-gradle-resources-and-metadata.3 citations.