Merge pull request #238 from SynapticNulship/hashdb_sqlite

Hashdb sqlite
Updated comments and a code layout
Moved hashdb files around a bit
fixed compile bug in hashdb / JNI
Added stubs to JNI java class, deprecated methods we don't want to support any more, added hashDB methods that are named more consistently.
Added other hash values to add method
Set db_name based on filename if the index type is SQLite (for now).
Comment updates.