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Consider transitives when identifying project dependencies
Previously, when building a layered jar, the Gradle plugin only considered a configuration's direct dependencies when identifying project dependencies. This resulted in transitive project dependencies being missed when deciding which dependencies belong in the application layer. This commit updates ResolvedDependencies to consider all projects from the root project when collecting the IDs of local projects. This ensures that any project dependency, no matter where it appears in the dependency graph, is successfully identified. Fixes gh-25163
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