Added a Degraph based tests to identify package cycles and violations in layering.
Moved Collation to the core.query package, fixing dependency cycles. Moved IndexOperations and IndexOperationsProvider to the core.index package. fixing dependency cycles. Moved GeoJsonConfiguration to config package. Replaced the original version of these interfaces/classes with a deprecated version extending the new one, in order to not break the existing API.
Removed all references to Part.Type, except for those to maintain the existing API. API using Part.Type is marked as deprecated. It violates the layering, because nothing but "config" should access "repository". Tests added to MongoRegexCreator in order to facilitate the removal of Part.Type dependencies. Using the moved/new ExampleMatcherAccessor.
Related Tickets: DATACMNS-1097.
Original pull request: #470.
