Parallel construction. They use their real methods to identify the user, then once they know the user, specifically target them with simpler known methods to build evidence for the case. In the court filing, they present evidence that they've gained through known methods which don't work all that well unless you already have a suspect, but they actually caught the suspect using methods that are not public (and won't become so, unless there's an internal leak at the FBI).
But if they were using parallel construction, surely the criminal complaint wouldn't make claims they can't prove using the non-secret chain of evidence, right? Here the court filing alleges that the FBI knows what IP address the defendant used to visit a Tor hidden service. Don't they now have to prove that claim if they want the prosecution to succeed?
They also know what specific pages on the offending websites they accessed.
I'm wondering if the classified document wasn't about tor, but about the 'implants' aka malware that were leaked in the same set of Snowden documents.
I think as much as tor being broken in some fixable way, they'd like it known even less that the FBI installs malware on the devices of persons of interest who haven't been convicted of anything.
If they truly can't break Tor and they deem the person of interest important enough for "national security" then I don't think anyone who has studied history, American or otherwise, believes that they are going to throw their hands up and say "welp, that's it."
Or in the case of Ross Ulbricht, just makes up a story about how he was trying to kill someone by suggesting the idea to him. Then uses that to justify an investigation that just happens to be a dead-end but conveniently gathers a bunch of other evidence that is relevant to another case.
I think it's commonly known, maybe not proven, but also it's a case of can they? yes. Would they? yes. As long as you agree with those two premises it's pretty likely
Genealogists use parallel construction to build out their families. Data from a large variety of sources gets used to indicate and corroborate individuals.
It's rather annoying that the initial knee jerk reaction to any negative take on authoritarian government action is labeled as a conspiracy theory to try to discredit it.
The CIA did a great job getting that word out there. It's sad it's used to dismiss credible and logical conclusions so readily.