Federal Bureau of Investigation Director James Comey’s recommendation that no charges be brought against Hillary Clinton for her use of an unclassified email server while secretary of state is significant, but what he did not address is equally important.

U.S. Democratic presidential candidate Hillary Clinton speaks during a "Get Out to Caucus" rally in Council Bluffs, Iowa January 31, 2016, one day before Iowa's first-in-the-nation caucus. REUTERS/Brian Snyder

What was not said about intent

Comey stated some 110 emails were classified when they were transmitted and received via Clinton’s personal email server. Comey stressed that he did not find evidence that Clinton intended to violate any laws, or that her actions rose to “gross negligence.” He did not explain the rationale behind this finding.

There was no electronic connection between the government’s classified systems and Clinton’s unclassified server. This indicates that on 110 separate occasions Clinton and/or one of her correspondents had to have retyped – or copied and pasted – information from a classified format; there is no other method to transfer data. Classified markings (i.e., “Top Secret”) were removed in the process (though Comey did say some marked classified emails were also found on the server).

The Inspector General for the Intelligence Community stated some of the documents were marked at the highest levels, including one about North Korea’s nuclear weapons program. At least 47 of the Clinton emails released contain the Freedom of Information Act release exemption B3 CIA PERS/ORG, which indicates the material referred to CIA personnel matters. Some emails show semi-oblique references to CIA staffers, known as “talk arounds,” to avoid mentioning a name or position per se.

Comey made clear the sensitivity of some of the information, saying “seven e-mail chains concern matters that were classified at the Top Secret/Special Access Program level when they were sent and received. These chains involved Secretary Clinton both sending emails about those matters and receiving emails from others about the same matters. There is evidence to support a conclusion that any reasonable person in Secretary Clinton’s position... should have known that an unclassified system was no place for that conversation.”

Whether information was marked or unmarked is irrelevant. Standard Form 312, signed by Clinton and every security clearance holder in the government, specifically notes that the laws apply to both marked and unmarked classified material. The legality of retroactive classification has been tested by the Supreme Court, which let stand a lower court decision that the practice was legal.

While Comey maintains there was no intent or gross negligence by Clinton to violate the law, it is difficult to reconcile her actions and his statement.

What was not said about perjury and obstruction

Hillary Clinton’s earliest statements, that no classified information traversed her server, later changed to “no marked” classified information. Comey explained emails found in others’ inboxes, messages not turned over by Clinton to the State Department, were work-related. Clinton claimed she turned over all work-related emails. Despite this, the questions of perjury and obstruction of justice were not addressed.

In addition, Comey stated Clinton’s lawyers deleted all emails they did not turn over to the State Department and then cleaned their devices in such a way to preclude complete forensic recovery. He added “It is also likely that there are other work-related e-mails that they did not produce to State and that we did not find elsewhere.” None of this was addressed in the context of destruction of evidence.

What was not said about precedent

The standards applied in the Clinton case are at variance with how classified information violations elsewhere in the government are handled.

As examples, the cases of CIA officer John Kiriakou (who served three years in federal prison for exposing a single, unmarked, unclassified business card with the name of a CIA employee), and TSA air marshal Robert Maclean (fired for exposing a text retroactively classified) stand out. Major Jason Brezler, who sent classified information to fellow Marines in Afghanistan to warn them about a Taliban conspirator, was forced out of the service. Even General David Petraeus, who transmitted classified information via his Gmail account to his mistress, received limited legal punishment and was forced to resign.

But perhaps with an eye toward others mounting a future national security violation “Hillary defense,” Comey did add “To be clear, this is not to suggest that in similar circumstances, a person who engaged in this activity would face no consequences. To the contrary, those individuals are often subject to security or administrative sanctions. But that is not what we are deciding now.”

What was not said about the Freedom of Information Act

Comey did not discuss Clinton’s actions and the Freedom of Information Act.

During her tenure as secretary of state and for some time afterwards, the State Department maintained it had no Clinton email records to produce in response to requests. Those statements – while technically true in that State could not search Clinton’s personal server – blocked journalists, private citizens, and for a time, Congress, from documents they were lawfully entitled to see.

The State Department’s own inspector general found these actions to be in contravention of the Federal Records Act.

What will be said

The director of the FBI labeled the leading contender for the presidency and her staff as “extremely careless” in their handling of America’s secrets. In the current political climate, this is generally seen as positive news by Clinton supporters, the new standard apparently being “not under indictment.” The Trump campaign will no doubt make this all a major focus of its messaging going forward.

Few believed, rightly or wrongly, that Hillary Clinton would face criminal charges over her handling of classified material. Yet, the questions not addressed by the FBI remain. Even if the majority of voters in November see the issue as put to rest, Republicans in Congress will be unlikely to feel the same come January.

(Disclosure: Following the publication – during Clinton’s time as secretary of state – of my book critical of the State Department’s role in the Iraq War, the department unsuccessfully carried out termination proceedings against me. Instead, I retired voluntarily.)