IAEA wants to make sure that there is no active military nuclear program in Iran. And IAEA deals with Iranian Nuclear program. No need to inject word "civilian" here. Iranians should not have anything not civilian in the first place.
As usually you demonstrate lack of any understanding about documentation, what agencies do, and being google handicapped resort to irrelevant strawman "arguments" and stupid claims. Which are not true.
No they haven't. All this crap is just yours assertions. Wrong as usually.
The current core document describing IAEA relations with Iran is GOV/2011/65 (there are newer of course, but they refer for details to this one). This details are accumulated in an annex dully named
Possible Military Dimensions to Iran’s Nuclear Programme.
Since you're google handicapped I'll suppress my promise to good friend of not giving direct links (and in such way not helping students to do quick and sloppy essays.)
http://www.iaea.org/Publications/Documents/Board/2011/gov2011-65.pdf
The core activities were from the start controlled by Mohsen Fakhrizadeh. Senior officer of IRGC. In this report IAEA starts with AMAD plan because PHRC (also controlled by him) didn't have clear nuclear activities.
I will quote some relevant pieces (far from exhaustive list, I recomend anybody interested in this problem to read document's annex)
The organizational arrangement of iranian nuclear program:

"... 22. According to the Agency’s assessment of the information contained in that documentation, the green salt project (identified as Project 5.13) was part of a larger project (identified as Project 5) to provide a source of uranium suitable for use in an undisclosed enrichment programme. The product of this programme would be converted into metal for use in the new warhead which was the subject of the missile re-entry vehicle studies (identified as Project 111). As of May 2008, the Agency was not in a position to demonstrate to Iran the connection between Project 5 and Project 111. However, subsequently, the Agency was shown documents which established a connection between Project 5 and Project 111, and hence a
link between nuclear material and a new payload development programme...."
"..24. The Agency has other information from Member States which indicates that some activities previously carried out under the AMAD Plan were resumed later, and that Mr Fakhrizadeh retained the principal organizational role, first under a new organization known as the Section for Advanced Development Applications and Technologies (SADAT) 28, which continued to report to MODAFL, and later, in mid-2008, as the head of the Malek Ashtar University of Technology (MUT) in Tehran.29 The Agency has been advised by a Member State that, in February 2011, Mr Fakhrizadeh moved his seat of operations from MUT to an adjacent location known as the Modjeh Site, and that he now leads the Organization of Defensive Innovation and Research.30 The Agency is concerned because some of the activities undertaken after 2003 would be highly relevant to a nuclear weapon programme..."
26.
In addition, throughout the entire timeline, instances of procurement and attempted procurement by individuals associated with the AMAD Plan of equipment, materials and services which, although having other civilian applications, would be useful in the development of a nuclear explosive device, have either been uncovered by the Agency itself or been made known to it.32 Among such equipment, materials and services are: high speed electronic switches and spark gaps (useful for triggering and firing detonators); high speed cameras (useful in experimental diagnostics); neutron sources (useful for calibrating neutron measuring equipment); radiation detection and measuring equipment (useful in a nuclear material production environment); and training courses on topics relevant to nuclear explosives development (such as neutron cross section calculations and shock wave interactions/hydrodynamics).
"...29. Information made available to the Agency by a Member State, which the Agency has been able to examine directly, indicates that Iran made progress with experimentation aimed at the recovery of uranium from fluoride compounds (using lead oxide as a surrogate material to avoid the possibility of uncontrolled contamination occurring in the workplace).
30. In addition, although now declared and currently under safeguards, a number of facilities dedicated to uranium enrichment (the Fuel Enrichment Plant and Pilot Fuel Enrichment Plant at Natanz and the Fordow Fuel Enrichment Plant near Qom) were covertly built by Iran and only declared once the Agency was made aware of their existence by sources other than Iran. This, taken together with the past efforts by Iran to conceal activities involving nuclear material, create more concern about the possible existence of undeclared nuclear facilities and material in Iran...."
"...44. The Agency has strong indications that the development by Iran of the high explosives initiation system, and its development of the high speed diagnostic configuration used to monitor related experiments, were assisted by the work of a foreign expert who was not only knowledgeable in these technologies, but who, a
Member State has informed the Agency, worked for much of his career with this technology in the nuclear weapon programme of the country of his origin. The Agency has reviewed publications by this foreign expert and has met with him. The Agency has been able to verify through three separate routes, including the expert himself, that this person was in Iran from about 1996 to about 2002, ostensibly to assist Iran in the development of a facility and techniques for making ultra-dispersed diamonds (“UDDs” or “nanodiamonds”), where he also lectured on explosion physics and its applications..."
this member state is Russia btw.
etc. etc. etc.
Now the second part: UNSC. Corresponding resolution is obviously Resolution 1929 (2010).
http://www.iaea.org/newscenter/focus/iaeairan/unsc_res1929-2010.pdf
"... Noting with serious concern the role of elements of the Islamic Revolutionary Guard Corps (
IRGC, also known as “Army of the Guardians of the Islamic Revolution”), including those specified in Annex D and E of resolution 1737 (2006), Annex I of resolution 1747 (2007) and Annex II of this resolution, i
n Iran’s proliferation sensitive nuclear activities and the development of nuclear weapon delivery systems,..."
This is direct comment on your ASSumption
and a cookie:
"..Noting with serious concern that Iran has constructed an enrichment facility at Qom in breach of its obligations to suspend all enrichment-related activities, and that Iran failed to notify it to the IAEA until September 2009, which is inconsistent with its obligations under the Subsidiary Arrangements to its Safeguards Agreement..."