This has been, and is being tried--as publicly evidenced by the abduction of two French security advisors last year. You're right, however, that security in Somalia--if it ever comes--will have to rest on Somali shoulders.
It doesn't help, of course, that not all of the TFG troops are sure what side they are on, or necessarily care!
As for the Ugandans, they have had some moderate (but limited) successes against the LRA. However, as northern Uganda has become increasingly less hospitable, the LRA have moved between south Sudan, DR Congo, and the CAR--which complicates things immensely.
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