There are recent revelations about the Syrian site, which was bombed by Israel in September, 2007, and why the Israelis knew it was a nuclear research facility under construction. It all began when an Iranian general, and former deputy defense minister (Ali Reza Asghari) defected in February of 2007. He said that Iran was financing a North Korean effort to help Syria develop nuclear weapons. The site had already been noted by American intelligence, but they were unsure of what it was. It seems that the Syrians had taken extraordinary security measures. No cell phones were allowed on the site, and all messages to and from the workers there were delivered in written form, by courier. In August, 2007, the Israelis sent in a twelve man commando team, by helicopter, to the site. Photographs, and soil samples, were taken. This confirmed that nuclear research was taking place at the site. The bombing mission followed the next month. American and Israeli intelligence concluded that Iran had spent over a billion dollars (much of it to North Korea) to finance the operation. Some intelligence officials doubt this, but Syria hasn't got much cash, and North Korea does not do freebies. Iran has the money and the motivation.
After the bombing, the Syrians promptly removed the structures, both the ones that were bombed and those left intact. Syria has since rebuilt the area with what appears to be a missile control and launching center. After the bombing, and accusations of nuclear weapons research, UN inspectors found that there were traces of uranium and graphite, indicating that there was indeed a nuclear research activity, at the very least, going on. The Syrians apparently did not realize that it was difficult, nearly impossible, to clear away the microscopic evidence that nuclear research was going on there.
North Korean technicians were involved with whatever was going on there, although Syria denied any nuclear work was taking place. Denying that North Koreans were around was more difficult, as North Koreans have been seen entering and leaving this area for months. North Korea is believed to be still selling weapons, and possibly nuclear technology, to Syrian mentor Iran. Moreover, the minute nuclear and graphite material can be traced back to where it came from, which in this case was North Korea.