Return manifest.Manifest from the Manifest() function without
serializing. The caller then has to call the manifest.Serialize()
function using the depsolved packages.
This moves towards changing the order of actions required to generate a
manifest. With this change, the manifest creation and depsolving can be
done independently, but this still requires instantiating the manifest
object twice (InstantiateManifest() is called in PackageSets() and
Manifest()), which we don't want to have to do.
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