For all the hand-wringing about overzealous punditry, the Mueller report was by and large an affirmation of the mainstream media’s investigative reporting. Almost all the big stories were confirmed in the report.

It confirmed that President Trump tried to fire special counsel Robert S. Mueller III, asked FBI Director James B. Comey for leniency on Michael Flynn, invited Comey to the White House where Comey said Trump asked him for loyalty, was pursuing business dealings in Russia in 2016 and was behind Donald Trump Jr.’s misleading explanations of the Trump Tower meeting. Other stories that proved ahead of their time included the digging into Paul Manafort’s foreign entanglements, Flynn being vulnerable to blackmail for lying to the White House, Trump asking intelligence chiefs and others to clear him in the Russia probe, Manafort meeting with a Russia-tied business associate during the campaign and the Trump team encouraging potential back channels with Russia.

In fact, pretty much every story confirmed by multiple big outlets tracks with what we see in the report.

At the same time, there have been a number of big stories that have long been in question, because other outlets couldn’t confirm or because they were tenuous. The Mueller report allows us to revisit some of them.

The BuzzFeed Cohen story

The story: This was a big one. BuzzFeed News reported that Trump had “directed” Cohen to lie to Congress about the Trump Tower Moscow deal. If true, it would have meant that Trump had committed the crime of suborning perjury. Other outlets, including this one, wrote about what the report would mean if it were true, but couldn’t confirm it. Then the special counsel’s office put out an unprecedented statement disputing it.

What Mueller says: “Cohen did not recall talking to the President about the specifics of what the statement said or what Cohen would later testify to about Trump Tower Moscow. He recalled speaking to the President more generally about how he planned to stay on message in his testimony.”

What it means: This is all according to what Cohen could recall. But he has flipped on Trump, meaning he has no reason to protect the president. It’s also notable that Mueller doesn’t directly accuse Trump’s personal counsel, who was frequently in contact with Cohen about his statement, of “directing” Cohen to lie. BuzzFeed issued a statement Thursday acknowledging Mueller’s interpretation differs from that of its sources.

Michael Cohen in Prague

The story: McClatchy reported Mueller had evidence Cohen might have been in Prague in the summer of 2016. That would have been big, because it echoed a claim in the Steele dossier that Cohen had met with Russians there to strategize about the 2016 campaign. McClatchy also later reported that Cohen’s cellphone had pinged a tower near Prague at the time.

What Mueller says: “ . . . Cohen understood Congress’s interest in him to be focused on the allegations in the Steele reporting concerning a meeting Cohen allegedly had with Russian officials in Prague during the campaign. Cohen had never traveled to Prague and was not concerned about those allegations, which he believed were provably false.”

What it means: McClatchy has added editor’s notes to its stories, stating, “Robert S. Mueller III’s report to the attorney general states that Mr. Cohen was not in Prague. It is silent on whether the investigation received evidence that Mr. Cohen’s phone pinged in or near Prague, as McClatchy reported.” McClatchy never actually reported Cohen was in Prague — just that evidence existed raising that possibility — and it’s still possible its reporting was accurate. In addition, the footnotes show Mueller’s source for Cohen never traveling to Prague was Cohen himself, with no other sourcing listed. This would seem to have been something Mueller would try hard to prove given its implications for potential collusion, but his report doesn’t shed much light on it.

(Also notably: While the Mueller report says “Cohen had never traveled to Prague,” Cohen has in the past told Mother Jones and the Wall Street Journal that he was there briefly in the early 2000s. He told The Washington Post at another point that he had driven through the city without stopping around the same time. He never said, though, that he had been there in 2016.)

Alfa Bank

The story: Slate published a lengthy story on the eve of the 2016 election with the provocative headline: “Was a Trump Server Communicating With Russia?” It reported that a server at a Russian bank called Alfa Bank had been connecting with a server linked to Trump in a way that some researchers thought unusual and suggested interpersonal communication.

What Mueller says: While the report makes several mentions of Alfa Bank -- including about how executives sought to make contact with the Trump team during the transition period -- none of them addresses these servers’ interactions.

What it means: As with Prague, it would seem this would have been something of significant interest to Mueller, if true. The fact that he didn’t address it suggests it didn’t mean much of anything — just as The Post Philip Bump predicted almost immediately back in 2016.

Paul Manafort and Julian Assange

The story: The Guardian reported in December that Manafort had “secretive” talks with WikiLeaks founder Julian Assange in the Ecuadoran Embassy in London in 2013, 2015 and the spring of 2016 — during a time Manafort was on the Trump campaign. That would be huge on the collusion front, given WikiLeaks would just months later release hacked Democratic emails meant to benefit the Trump campaign.

What Mueller says: Nothing.

What it means: Again, this would seem to be something Mueller would have been very interested in, if it were true. Both Manafort and WikiLeaks denied it. And no other outlet has confirmed it.

The Republican Party platform on Ukraine

The story: During the 2016 Republican National Convention, the official party platform was softened to remove support for arming Ukraine against Russia and instead advocated “appropriate assistance” and “greater coordination with NATO defense planning.” Washington Post opinion writer Josh Rogin broke the news of the plank being “gutted” by the Trump campaign. The Los Angeles Times reported that Trump “surrogates” had intervened to make the change. After Manafort denied the Trump campaign was behind the change, the Daily Beast quoted GOP delegates who said it was indeed done by the campaign.

What Mueller says: “The investigation did not establish that one Campaign official’s efforts to dilute a portion of the Republican Party platform on providing assistance to Ukraine were undertaken at the behest of candidate Trump or Russia.”

What it means: The reporting was correct that the campaign was behind it. Plenty of people have drawn further conclusions based upon that reporting, suggesting that Trump himself was behind it or that it might have been a favor to Russia. The stories linked above did not make such accusations. It is worth emphasizing, though, that Mueller says he did not find evidence for some of those more nefarious theories.

Oleg Deripaska and “caviar”

The story: In July 2016, Manafort’s associate in Ukraine, Konstantin Kilimnik, wrote him to say, “I met today with the guy who gave you your biggest black caviar jar several years ago.” The Washington Post, which first reported on the email, cited anonymous congressional investigators who said they believed the “caviar” reference was to Oleg Deripaska, a Russian oligarch with close ties to Vladimir Putin. Other reports, including the Guardian and Business Insider, went on to state it as fact that it referred to Deripaska. But in a later statement to The Post, Deripaska denied ever interacting with Kilimnik. I made an argument at the time that it was plausible it was not, in fact, Deripaska, based upon how Kilimnik described “caviar” guy.

What Mueller says: Manafort told Mueller it wasn’t Deripaska, but that it was instead former pro-Russia Ukrainian president Viktor Yanukovych. And that seems to check out to Mueller. “Manafort identified ‘the guy who gave you your biggest black caviar jar’ as Yanukovych. He explained that, in 2010, he and Yanukovych had lunch to celebrate the recent presidential election. Yanukovych gave Manafort a large jar of black caviar that was worth $30,000 to $40,000. Manafort’s identification of Yanukovych as ‘the guy who gave you your biggest black caviar jar’ is consistent, with Kilimnik being in Moscow — where Yanukovych resided — when Kilimnik wrote ‘I met today with the guy’ and with a December 2016 email in which Kilimnik referred to Yanukovych as ‘BG,' [REDACTED]."

What it means: The congressional investigators were apparently wrong, though Mueller doesn’t quite state as fact that it was Yanukovych. Reports that said definitively that it was Deripaska proved incorrect.

Kilimnik and Deripaska’s jet

The story: Flight records have shown a private jet belonging to Deripaska landed in Newark shortly after Manafort’s Aug. 2, 2016, meeting with Kilimnik. The plane returned to Moscow shortly thereafter. Independent journalist Scott Stedman first spotted the flight records, which were notable given Manafort’s past work for Deripaska and apparent efforts to recoup money he believed Deripaska owed him. Vice News later offered an “exclusive” the suggested a possible connection and said “that August flight has caught the attention of congressional investigators, in part because of its timing.” Some have concluded that perhaps Kilimnik was flying on Deripaska’s plane, but Deripaska has denied it and told The Washington Post that he never interacted with Kilimnik.

What Mueller says: “Deripaska’s private plane flew to Teterboro Airport in New Jersey on the evening of August 2, 2016. According to Customs and Border Protection records, the only passengers on the plane were Deripaska’s wife, daughter, mother, and father-in-law, and separate records obtained by our Office confirm that Kilimnik flew on a commercial flight to New York.”

What it means: The question wasn’t whether Kilimnik flew to the United States on Deripaska’s plane (given the plane arrived after his and Manafort’s meeting) but whether he might have departed on it. Mueller’s report does not address that. But there is still no evidence that that’s what happened.

Kilimnik told The Post last week after the Mueller report’s release that he flew commercial. “This is one of the craziest inventions in the whole flow of insanities about me,” he said. “I absolutely and vehemently deny that I flew back from the U. S. on Mr. Deripaska’s private plane.”

Tom Hamburger contributed to this story.