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KAMPALA, Uganda — The presidents of Sudan and South Sudan signed a long-awaited cooperation agreement on Thursday, paving the way for the resumption of oil exports and casting their ailing economies a desperately needed lifeline. But several analysts said the deal came up far short.

The status of Abyei, a contested border area, was not settled. Nor was that of several other disputed territories, differences that have driven the countries’ two leaders, historic enemies, nearly to all-out war.

“The seeds of further conflict are firmly planted in this partial deal,” John Prendergast, a co-founder of the Enough Project, an anti-genocide organization that watches the two Sudans closely, said by email.

Last year, amid great jubilation, South Sudan split off from Sudan after decades of guerrilla struggle. But the divorce was messy. Forces from the two countries have battled intensely over the past year amid confusion over disputed areas and contested oil fields.

South Sudan has billions of barrels of oil, but the pipeline to export it runs through the north. The south shut down production last winter, which deeply wounded the economies on both sides of the border, leading to skyrocketing inflation, protests and rising discontent.

Since then, negotiations have gone around and around, with increasing pressure by the U.S., the African Union and the United Nations to come to an agreement.

Since Sunday, Omar al-Bashir, the president of Sudan, and Salva Kiir, South Sudan’s leader, had been holed up together in negotiating rooms in Addis Ababa, Ethiopia, trying to hammer out a compromise. For years, the two men fought each other on the battlefield, and it seems that the history of bitterness has been extremely difficult to overcome.

On Thursday, al-Bashir and Kiir emerged to announce that they would demilitarize the border — a step that had been agreed to in principle last year but was almost instantly violated when Sudan began a brutal counterinsurgency campaign in the Nuba Mountains, near the border. The two sides also committed to resuming cross-border trade and allowing citizens from each side to move freely.

And they agreed to resume oil production — again, an issue that had been previously covered, with a deal reached in August, but had not yet taken effect because of mutual mistrust.

“This basically kicks the can down the road,” said EJ Hogendoorn, the Horn of Africa director for the International Crisis Group, a conflict-prevention organization.

One person close to the talks tried to put a positive gloss on them, saying the negotiating session was a “crunch summit” and the border deal was “serious progress.”