Expert American opinion on the outcome of last month’s nuclear negotiations with Iran is sharply divided. Those who want Iran to give up all enrichment technology are relieved that a “bad” deal was averted. Pressure is building in Congress, especially but not exclusively among Republicans, for new sanctions. Some would like to see Congress authorize the use of military force. Others think an interim arrangement limiting Iranian enrichment (the November 2013 “Joint Plan of Action,” which took effect January 20, 2014) is good enough for now and certainly better than no limits. They resist the idea of new sanctions and hope for an agreement by the new July 2015 deadline that will provide as much as a year’s warning of any Iranian moves to produce the material needed for a nuclear weapon.
Both perspectives focus on the overt Iranian nuclear program, which is monitored and safeguarded by the International Atomic Energy Agency (IAEA) under provisions of the Nonproliferation Treaty (NPT). But no country since the IAEA was founded in 1957 has used an overt program or safeguarded material to obtain nuclear weapons. Nuclear powers India, Pakistan, and Israel never signed the NPT. North Korea signed but withdrew before testing a nuclear weapon, using material produced clandestinely. South Africa developed and tested nuclear weapons clandestinely before it became an NPT signatory in 1991, when it gave them up. Belarus, Ukraine, and Kazakhstan had many Soviet nuclear weapons on their territory but transferred them out and joined the NPT in the 1990s, after the Soviet Union collapsed.
It is hard to avoid the conclusion that clandestine and non-safeguarded nuclear programs are a much greater risk for proliferation than the ones the IAEA monitors.
Iran is an NPT signatory. Its safeguarded facilities are in compliance with its NPT obligations. It is also in compliance with the Joint Plan of Action. But Iran has not implemented all resolutions of the IAEA Board of Governors or the UN Security Council, nor has it implemented the Additional Protocol that permits short-notice inspections of suspect locations. The IAEA’s bottom line is ominous:
The Agency is not in a position to provide credible assurance about the absence of undeclared nuclear material and activities in Iran, and therefore to conclude that all nuclear material in Iran is in peaceful activities.
The question of covert facilities is said to preoccupy some American negotiators, but the negotiations have focused on Iran’s overt, safeguarded program.
The clandestine route to a nuclear weapon is far more likely. The IAEA has asked Tehran to explain research efforts that IAEA scientists associate with nuclear weapons research, including initiation of high explosives (to compress fissionable material) and neutron transport calculations (required to initiate a chain reaction). Tehran has not yet provided a satisfactory response to these inquiries or access to facilities where unsafeguarded activities may have taken place in the past. American intelligence agencies have said publicly that they believe this weapons-related research ended more than a decade ago. But earlier efforts that betrayed “possible military dimensions” remain a source of profound distrust of Iranian intentions, not only in the United States but also in Israel and elsewhere.
Iranians are quick to respond that the Supreme Leader has issued a fatwa against production or use of nuclear weapons. This can be “secularized,” meaning it can be issued as legislation. They also emphasize that Iran would be far less secure if it obtained nuclear weapons but in the process triggered Saudi, Egyptian, or other efforts to match the prize. Far better, some say in private, to gain the underlying technology but stop short of weaponizing, which is an expensive process of not only producing the weapons but also making them compact enough to be mounted on missiles and launched. 
Americans concerned about an Iranian clandestine nuclear program want Tehran to “come clean” about its past activities. This is what Muammar Qaddafi did in 2003, when he opened up Libya’s clandestine (but still rudimentary) nuclear program to intense American scrutiny and removal. It is difficult to picture Iran doing as much as that. But it could, and should, go much further than it has so far in answering frankly the IAEA’s pointed questions about its past weapons-related research and development.
The United States can hope that the current negotiations on Iran’s overt nuclear program will put a year between any decision to get nuclear weapons and the result, in exchange for some measure of sanctions relief. It has to aim to do at least that well on the clandestine side as well. This will mean not only Iranian implementation of the Additional Protocol that allows surprise inspections, but also a clear and comprehensive account of past weapons-related nuclear research and development.