DependencyGraphBuilder to take managedDependencies

(not yet started)

If DependencyGraphBuilder, which currently has only `repositories` field, takes managedDependencies, then we can simulate linkage errors that would appear when a project uses a BOM and depends on particular Maven artifacts. For instance, we can simulate linkage errors generated by a project that uses `com.google.cloud:libraries-bom:3.4.0` with dependencies of `org.apache.beam:beam-sdks-java-core:2.18` and `com.google.cloud:google-cloud-kms`.

Such simulations help to ensure there's no linkage conflicts **caused by combining** Apache Beam and libraries-bom. Each of the libraries has some linkage errors, such as appengine-api-sdk.