Do not duplicate references in reference table

Do not insert duplicate records into the references table. Fixes problem with (most of) current failing tests.

I think ultimately we should reuse the transports own logic for storing nodes similar to [what happens in Jackalope FS](https://github.com/jackalope/jackalope-fs/blob/master/src/Transport/Fs/Test/FixtureGenerator.php#L32)