Today, Federal Bureau of Investigation Director James Comey announced the end of the FBI’s investigation into former Secretary of State Hillary Clinton’s use of a personal email server.

“Although we did not find clear evidence that Secretary Clinton or her colleagues intended to violate laws governing the handling of classified information, there is evidence that they were extremely careless in their handling of very sensitive, highly classified information,” Comey said.

The FBI’s public recommendation to the U.S. Justice Department that Secretary Clinton not face criminal prosecution suggests that, barring further revelations about security or newly discovered email, the issue is now unlikely to significantly disrupt the presidential campaign.

At the story’s core, however, are questions that remain about how digital information is managed and regulated in government. Here are five questions that will endure beyond the political interest:

1) Can the Freedom of Information Act (FOIA) be protected from intentional obfuscation, especially by those with the most power?

The available evidence suggests that Clinton intentionally tried to control whether email was exposed to discovery under FOIA. Today’s recommendations from the FBI reinforce a sense that trying to evade FOIA is wrong but isn’t illegal, weakening the idea that records should be managed in a way that upholds public access. More recent legal reforms requiring official email use are important, but ultimately incidental to the more fundamental question: Do we expect public officials to conduct their work in a manner that is generally accessible to the FOIA and to congressional oversight? How can such an expectation be enforced?

2) How will transparency be affected by the escalating concerns over hostile actors?

The FBI found that the setup that staff created for Clinton used multiple servers and was insecure. As a result, the department’s assessment is that it is possible that hostile actors gained access to the email account. That’s far short of evidence that a nation state or non-government actors accessed the messages or benefited from them, though the specific details the director shared are understandably opaque. The larger issue of security in federal government merits continued oversight and aggressive reforms that focus upon finding and closing vulnerabilities and identifying and encrypting sensitive data. The compromise of background checks and biometric data held by the Office of Personnel Management show exactly what’s at stake here.

As recent debates over the Stop Online Piracy Act (SOPA), net neutrality and encryption have demonstrated, our politics is generally inadequate at understanding technically complex issues. Unfortunately, government agencies have sometimes not been far behind. Every question of transparency and accountability we ask today is downstream from a separate set of often imperfect, inadequate, temporary fixes to systems. Security and privacy for technical systems cannot be afterthoughts nor checked off of a list: they must be by design and default.

3) How can records management be improved when technology is making it harder?

Records management is an extremely important, out-of-date, and a multi-decade problem. The FBI found that Clinton’s staff wasn’t archiving her email server, even though it was being used for public business. Director Comey said that the FBI has reasonable confidence, however, that there was no intentional misconduct in the sorting efforts prior to turning over Clinton’s email. This informs the decision regarding prosecution for criminality but not trust in the outcome. Records management is difficult, and can even be burdensome, but it’s a cornerstone of open government, oversight and the rule of law. The requirement that Clinton responsibly manage records existed long before her tenure in the State Department, but in a largely unenforceable sense mandated by recommendations from the National Archives.

From cloud-based email to encrypted chat to ephemeral messaging, public officials now have both means and incentive to conceal conversations from scrutiny. Clinton’s case is only the most high-profile example. If government agencies do not respond aggressively to the proliferation of electronic records and messaging systems, the situation will become far worse before it gets better, and neither side will budge. Officials will expect to use familiar tools that create an unmanageable flood of records, while public expectations and accountability require them not to do so.

4) How does this backdrop affect potential whistleblowers?

When Comey said that no reasonable prosecutor would bring a case against Clinton, it may have come as a surprise to whistleblowers or lower-level government workers and military who have been aggressively prosecuted for mishandling classified information. Politico’s review of similar cases, though, very helpfully explains that similar cases that were prosecuted all have additional aggravating factors. To what extent does the enforcement of classification laws create a bias against (otherwise lawful) dissent, and become a tool that harms whistleblowing, and the clear public interest it often represents?

5) What effect will this have on trust in government?

Over the longer term, the next president should embrace a higher standard for open government. In the short term, our politics will obsess over the details of this case and investigation, but what will matter more is how we use what we’ve learned to build a stronger, more open and accountable system.

This week, the public saw a government institution function in the face of remarkable pressure. It appears that FBI has successfully completed an extraordinarily high-profile, independent investigation of a major party’s presumptive presidential nominee in an election year that could have led to criminal charges without any sign of political involvement. (Attorney General Loretta Lynch’s meeting with President Bill Clinton was clearly ill-advised, but falls far short of evidence of political involvement.) For all the talk of American political dysfunction, it’s worth observing that for many countries such a feat may have proved impossible.