Prepare FileManager for removal from public API.

This is preparation work for a clearup of FileManager.

Applications should not be using (jena-core) FileManager directly - there is equivalent functionality for remapping in RIOT and the read caching is  separated out in RIOT.

Long term, FileManager can be removed from general use. It is used by the OntDocumentManager so making solely for that purpose, maybe moving it to the "ont" sub-system.

The first step is to mark access via FileManager.get() as deprecated to signal future change. Also, mark the operations "readModel", "loadModel" that are better done with RDFDataMgr anyway.

Within Jena, clean up and switch to an access function that has the name "Internal" in it : FileManager.getInternal()

There are assemblers for FileManager and (jena-core) LocationMapper. We don't have an easy way to signal deprecation. They are used for OntDocumentManager. 

In the documentation:

• documentation/notes/file-manager.html

• assembler: only mention in the documentation for OntDocumentManager assembly.

and a few mentions in usage examples elsewhere.