UPDATE:

The ICG has a good report on the simmering conflicts in Sudan and South Sudan:

The loss of South Sudan has had a profound effect on the NCP, and senior generals led a soft-coup within the party. They have outflanked more pragmatic elements in the NCP who seek a negotiated strategy. Encouraging progress in the post-separation arrangements between North and South was blocked. More importantly, hardliners in Khartoum — including SAF generals — immediately rejected a 28 June framework agreement, which includes a political and a security agreement for Southern Kordofan and Blue Nile, facilitated by former South African President Thabo Mbeki and Prime Minister Meles Zenawi of Ethiopia, and signed by Dr. Nafie Ali Nafie, Co-deputy NCP chairman and a presidential adviser. A few days later, President Omar al-Bashir publicly disavowed the agreement.

Check out the rest of the report here.

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Texas in Africa makes a compelling argument against arming South Sudan (against potential aggression from Khartoum). She basically outlines three reasons against arming Juba:

1. Such a move would implicitly side with the SPLM against other domestic armed/opposition groups. The point of concern here is that having just won independence South Susan needs to have a negotiated settlement among all interested groups. The Dinka-dominated SPLM, in particular, ought to credibly share power and resources with the other ethnic/interest groups.
2. Arming South Sudan would spark an arms race against Khartoum and might lead to a war sooner rather than later.
3. The West can’t be sure of Juba’s future geopolitical leanings. The same weapons might be used in the future against say America and its allies – AfPak style.

For the most part I agree with Laura. And like her, I am on record as having concerns over the alarmist celebrity diplomacy/mediation effort that has been orchestrated in South Sudan, Darfur and eastern DRC by Prendergast and his buddy Clooney.

In addition, I think that the debate over whether or not to arm Juba forecloses on other options that might also help secure South Sudan. Make no mistake, South Sudan has real domestic and international security challenges that occasionally will require the use of military force. Addressing these security challenges will necessarily require some form of military aid to South Sudan.

Here’s my take:

1. If South Sudan is to avoid the fate of Zaire/DRC, the pacification of the whole country must happen ASAP. While negotiating with rebel leaders is the best approach, the truth is that in some cases military force might be needed. To that end providing SPLM with the necessary capacity to win the fight against fringe groups that do not want to sit at the negotiating table may be a necessary evil. Yes, we should be cognizant of the fact that there are legitimate internal differences within South Sudan. But we should not legitimize any groups that might want to air those differences using the force of arms. Real democratic competition can only take place in a peaceful environment. Armed challengers to SPLA (the legitimate army of South Sudan) must bear the burden of proving the legitimacy of their grievances. South Sudan’s Savimbis must be deterred. Also, the international community must not be under any illusion that democracy will come soon to South Sudan. It will take a long time.
2. The arms race between Khartoum and Juba is already underway. The question is not if it will happen but what it will lead to. Furthermore, after “losing” the South and its oil Bashir will be hard pressed for distractions from his domestic woes, especially if the economy of Sudan experiences a sharp decline. Starting a border war with South Sudan would be a welcome distraction. Although arming the SPLA is not the best way to deal with this possibility, an alternative would be to bring in the EAC through a regional defense pact. Uganda, in particular, would be interested in such a deal since it would help reduce its own defense budget. The involvement of Eritrea in South Sudan’s internal conflicts makes the need for a regional security arrangement even more urgent. Most recently the UN accused Eritrea of plotting to bomb an AU meeting in Addis Ababa Ethiopia.
3. Concerns over Juba’s future geopolitical leanings can be allayed through continued military aid and professionalization. This can be achieved by getting the generals out of politics following the Kenyan model – a combination of awesome perks and professional training – and through greater political and economic integration of South Sudan into the East African Community.

War is nasty and should be the last option. That said, there is a need for genuine debate over how to achieve the twin goals of state monopoly of violence within South Sudan and the deterrence of a trigger-happy Khartoum.

If it were left to me I would quickly move to decouple the SPLM and SPLA as a condition for any military assistance. The last thing the region needs is yet another regime with a fused political and military leadership as is the case in Rwanda and Uganda.