JFK files release: What have we found out and what do we still not know?

The JFK files are now available. Sort of.

The documents have been released to the public but there are major omissions, and parts that still won't be understood for some time.

They are a major breakthrough, shedding light on one of the most momentous days in world history. They depict the confusion and cover ups that followed, and the strange events of that day.

Despite that, much still remains unknown. The files are going to take weeks to read through – and, more importantly, some of them have been kept hidden.

The JFK files that have been released paint a picture of a disorganised, confused, anxious US government and establishment as it attempted to deal with the fallout from the shooting. Nothing has yet pointed to a conspiracy, but plenty points to a worry that there was one: the documents show officials messaging each other to ask whether Lee Harvey Oswald was in the pay of the CIA, for instance – and not receiving an answer.

No smoking gun has yet been found that suggests there was anything untrue about the official sequence of events on that day in November. Nothing yet suggests that Lee Harvey Oswald didn't work alone, that he had killed JFK as part of a plot or that his own killing was part of a similar conspiracy.

What the documents do show is that the government had very little idea what was going on, and certainly considered all of those possibilities themselves. In the files are anxious letters that attempt to deal with the rumours that the assassination was something to do with Cuba, Russia, or another government, and the FBI's struggle to monitor further threats that might follow on from Oswald.

The files show that even the FBI is concerned about a conspiracy – and ensuring that nobody was worried that there actually was a plot beyond the official story. In one document, director J Edgar Hoover rants that "There is nothing further on the Oswald case except that he is dead."

But, reflecting on Oswald less than an hour after he died, Hoover already sensed theories would form about a conspiracy broader than the lone assassin.

"The thing I am concerned about, and so is (deputy attorney general) Mr. Katzenbach, is having something issued so we can convince the public that Oswald is the real assassin," he said. He also reported: "Last night we received a call from our Dallas office from a man talking in a calm voice and saying he was a member of a committee organized to kill Oswald."

Hoover said he relayed that warning to Dallas police and was assured Oswald would be sufficiently protected. Oswald was shot dead the next day by Jack Ruby.

But it's important to note that scholars say that it'll take weeks to go through the thousands of documents that have just been released. Many of them are very unimportant, and others' importance might not become fully clear until the full picture is put together – meaning that it might take a long time to fully piece together what the JFK files have to tell us about what happened.

An awful lot still remains mysterious, and not just because scholars haven't finished picking through the files. Of the 3,100 documents set to be released, 300 have been held back on the instruction of the US intelligence establishment – and there's no clue as to what's in them.

Donald Trump said he hadn't wanted to make the decision but that the files were a risk to national security. He gave agencies six months to sort through the files and argue for any that they think should still be kept secret.

But that decision has meant that far from putting conspiracy theories to rest, it has just served to spawn more. Some of the JFK files may never be released – and so the mystery and secrecy about what happened that day, and the ones leading up to and from it, could never truly end.

The last batch of assassination files included more than 3,100 documents — comprising hundreds of thousands of pages — that have never been seen by the public. About 30,000 documents were released previously with redactions. The National Archives released more than 2,800 documents on its website Thursday evening. But Trump delayed the release of the remaining files after last-minute appeals from the CIA and FBI. Trump cited "potentially irreversible harm" to national security if he were to allow all the records out now and placed those files under a six-month review. Officials say Trump will impress upon federal agencies that JFK files should stay secret after the six-month review "only in the rarest cases."

President George H.W. Bush signed a law on Oct. 26, 1992, requiring that all documents related to the assassination be released within 25 years, unless the president says doing so would harm intelligence, law enforcement, military operations or foreign relations. The push for transparency was driven in part by the uproar in the wake of Oliver Stone's 1991 conspiracy-theory filled film "JFK."

Additional reporting by agencies