For more than a decade, the C.I.A. has closely followed the workings of one Iranian officer and his sprawling nuclear empire: Mohsen Fakhrizadeh, the relentless driving force behind what Western intelligence agencies say was Iran ’s Manhattan Project, its effort to design a compact nuclear weapon that could fit atop a missile. Now, in the final push for a comprehensive nuclear agreement with Iran , accounting for the accomplishments of Mr. Fakhrizadeh and his team of university scientists, missile engineers and military officers is emerging as one of the last and most formidable obstacles — perhaps on a par with the question of whether inspectors will be able, on short notice, to step into any place they suspect […]