Remove more deprecated things

o Removed deprecated constructors in EmbeddedReadOnlyGraphDatabase
o Removed unused setting in OnlineBackup.
Removes all but one deprecated method in GraphDatabaseAPI.

Also fixes failing TestGuard test:

* The resolveDependency method is documented as throwing an IllegalArgumentException
   if the dependency cannot be resolved. The places that tries to resolve a dependency
   on Guard now correctly handles this possibility.
Make the UseJOTMAsTxManagerIT and the TestReadOnlyServer tests green

Also, we now allow ReadOnlyDatabaseProxy, when used through the shell,
to start transactions.

Also did some general clean-up in various places.
Merge pull request #1446 from jakewins/deprecated-again

Remove deprecated methods in GraphDatabaseAPI
ConsistencyCheck now waits for indexes to populate.
Revert "ConsistencyCheck now waits for indexes to populate."

This reverts commit b30bc81b5d45f510258e90b3d1b013a365bf4d84.