Kariem,
I checked this out myself and was unable to use most of the JPA tooling because of the absence of a concrete catalog and / or schema in SQLite. Since you mentioned you got it working for netbeans, I assume all references to the tables in annotations are unqualified (i.e. there is no catalog or schema attribute)?
I have filed a PR against this issue for investigation, but for now I cannot suggest any workaround. We’ll try and get this fixed in the 6.5 GA release, sorry for the inconvenience caused.