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The case caused uproar and sparked demonstrations across the Horn of Africa country.
The death deals a big blow to the militant group which in the past lost senior commanders in US airstrikes.
Johnson faces a potentially more fractious meeting later on Sunday when he will confront the European council leader.
In 2013, he refused to swipe t-shirts with an Israeli player in a display of support for Palestinian rights.
The President lauded Abdalla Hamduuk the new Prime Minister of Sudan on his appointment.
The surprise decision gives the long-sitting assembly extra time to remain in power and serve.