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