Israel may have done it for a few reasons:
1. To slow and reduce the amount of arms destined for the Gaza Strip
2. To practice a long range 1900 kilometer mission that would have some parallels to the effort to strike Iran's nuclear facility
3. To give credibility to the military option to strike Iran.
There's really only one country that has the capabilities or the motive to wage a pinpointed aerial assault on a single wing of a single weapons facility in the southern reaches of city of a 5 million people: Israel. The defense ministers of Sudan and Iran signed a "military cooperation agreement" in 2008. Sudan has hosted Iranian Revolutionary Guard personnel, and allegedly served as a transit point for weapons bound for Hamas, in the Gaza Strip.
Israel might have struck inside the Sudan before: once, in early 2009, when it allegedly destroyed a 23-truck weapons smuggling convoy in the country's east, and again in April of 2011, when Israel might have been responsible for the bombing of a Hamas arms trafficker in Port Sudan. Assuming it was also Israel's doing, the destruction of the weapons facility would represent another level of audacity. "I would say that if the Sudanese government's claims are correct, then this is longest strike -- the farthest strike -- ever executed by the Israeli air force," says Ehud Yaari, the Israel-based Lafer International Fellow at the Washington Institute for Near East Policy. "We are talking about something that is 1,800 or 1,900 kilometers [from Israel], depending on the route. That's farther away than the range from Israel to the main Iranian nuclear installations in Natanz and Qom."
Yaari hypothesizes that the facility was partly dedicated to the Iranian-assisted production of weapons headed for Gaza.
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