"seems Fitz knew the primary source....I wonder how ?"
I don't know. Fitz had a waiver, but he didn't necessarily know it was the primary source. Because even the primary source may not have known that he was Novak's primary source.
But he (the source) obviously does now, and so does Fitz.
The source may have given Novak the go-ahead to talk with Fitz, but not to disclose it in public, and not in print. Novak would be obliged to adhere to that (unless he wants to burn sources, which he'd never do, or else become a persona non grata in DC).
So the question is, why hasn't Fitz indicted the primary source?