For anyone interested in this topic there's a great book by investigative journalist Gareth Porter that details the whole saga: Manufactured Crisis: The Untold Story of the Iran Nuclear Scare
It should be pointed out that the evidence which both the US intelligence estimate and the IAEA rely on to determine that there was an Iranian nuclear weapons program prior to 2003 is the so-called "laptop documents" which are fairly clearly forged but for which there are political reasons to ignore that fact.
These forged documents had been used as the basis for a number of inspections by the IAEA of Iranian military facilities. The IAEA's inspections never found any evidence to substantiate the forged documents. Iran permitted such inspections even though they went above and beyond what Iran was required to permit under its NPT agreement. However given that these sorts of inspections were used by the US used to gather detailed targeting data on Iraqi facilities for the Gulf War Iran chose not to allow even more non-required inspections. That's the sole basis of the IAEA's 'concern' and the reason they keep bringing these forged documents up even though they've not been substantiated at all.
As part of the recent nuclear talks Iran insisted that these forged documents be put to rest and not brought up again in the future, which is what this report is supposed to be about.
The linked article by Ariane Tabatabai makes it sound like Iran has now admitted the existence of a nuclear weapons program, but this is false. Instead what Tabatabai is doing is essentially repeating the same cycle of making accusations on the basis of these forged documents and using the previous unsubstantiated accusations as the only 'substantiation'. For example Tabatabai writes:
The IAEA report unsurprisingly indicates that Tehran did have a “coordinated” nuclear weapon development program until 2003.
The report in fact says:
Information available to the Agency prior to November 2011 (i.e., the forged "laptop documents") indicated that Iran had arranged, via a number of different and evolving management structures, for activities to be undertaken in support of a possible military dimension to its nuclear programme. According to this information, the organisational structures covered most of the areas of activity relevant to the development of a nuclear explosive device. The information indicated that activities commenced in the late 1980s within Departments of the Physics Research Centre (PHRC) and later, under the leadership of Mohsen Fakhrizadeh, became focused in the early 2000s within projects in the AMAD Plan, allegedly managed through the ‘Orchid Office’. Information indicated that activities under the AMAD Plan were brought to a halt in late 2003 and that the work was fully recorded, equipment and work places were either cleaned or disposed of so that there would be little to identify the sensitive nature of the work that had been undertaken. Eventually, according to the information, a new organization known as the Organization of Defensive Innovation and Research29 was established by Mohsen Fakhrizadeh and based at the Mojdeh Site near Malek Ashtar University in Tehran.
The report goes on describing Iran's response:
In Iran’s submission of 15 August 2015 under the Road-map, Iran provided the Agency with information concerning a number of organisations described in the 2011 Annex (i.e., the forged "laptop documents") and on their relation and functions. In this regard, Iran, inter alia, denied the existence of a coordinated programme aimed at the development of a nuclear explosive device, and specifically denied the existence of the AMAD Plan and the ‘Orchid Office’ as elements of such a programme.
As far as I can tell the documents Iran submitted don't appear to be available so I'm not sure exactly what they say.
The Agency submitted questions to Iran on this subject on 8 September 2015, which were then discussed at technical-expert meetings in Tehran. A significant proportion of the information available to the Agency on the existence of organizational structures was confirmed by Iran during implementation of the Road-map.
Of course no further details are given as to what "a significant proportion" is, or what 'organizational structures' Iran confirmed and there's especially no indication that they were engaged in any nuclear weapons program. If Iran had confirmed that then that certainly would be explicitly described here. Since the report is vague on this point we can be pretty certain that Iran did not confirm that any such organization was involved in a nuclear weapons research and the report is simply leaving that out, likely so as to give an appearance opposite to the reality.
In the overall conclusion the report ends with
The Agency’s overall assessment is that a range of activities relevant to the development of a nuclear explosive device (but which the Agency acknowledges also have alternative applications, and for which there's no evidence that these activities actually were part of any nuclear weapons program) were conducted in Iran prior to the end of 2003 as a coordinated effort, and some activities (again, activities with non-nuclear applications and for which there's no evidence that they were undertaken for any nuclear weapons related purposes) took place after 2003. The Agency also assesses that these activities did not advance beyond feasibility and scientific studies, and the acquisition of certain relevant technical competences and capabilities. The Agency has no credible indications of activities in Iran relevant to the development of a nuclear explosive device after 2009.
So in essence there is no new information substantiating any of the previous allegations about a nuclear weapons program in Iran, and the only basis for such allegations remains the forged laptop documents.
Even taking the report's deceitful language at face value it should be clear just how far away from reality many of the accusations flying around are: Iran does not currently possess nuclear weapons, they do not have any secret uranium enrichment program, they are not engaged in working toward having a nuclear weapon, and even in the unlikely event that they ever decided that they should begin developing the technology for a nuclear weapon they would then have to engage in many years of work to do so and they could not do so without detection.