The USG inter-agency process* is dependent upon the planning capabilities of the Pentagon - and maybe it shouldn't be. Increasingly, the inter-agency process is the center of gravity for the United States' aggregate security capabilities (for simplifying reasons, let's stick here to the functional phases of conflict as conceptualized within US defense - phases zero to IV. Obviously, not all conflicts contain use of armed force). But only the US Department of Defense has extensive planning and business development sections working on generalized and concrete preparations for pre-conflict and post-conflict issues.
No-one doubts that the US rules phase III - major combat operations. But the US is not amassing the potential power it has for phases zero and IV. The latter refers to postconflict and the former to preconflict. To each of these belong at set of tasks that are more or less well-described and more or less well-understood. Post-conflict is a more well-described in terms of probable solutions and possibly better understood than pre-conflict. This is because post-conflict is more clearly a challenge for concrete organizations - ours, at least to begin with.
Post-conflict refers to both a complex organizational and logistic task (establishing country and government-wide administrative functioning organizations through military and civilian capabilities while/and handing them over to the host nation) and a strategic task namely identifying the wanted host national endstate, in fucntion of feasibility and ambitions (the choice is evidently shaped by political and anthropological both ramifications and limitations). To this effect, JFCOM has created the SSTR JOC which describes in general terms the challenges and is used as basis for doctrine development; Pentagon has issued the DoD Directive 3000.05, which sets SSTR Ops on par with major combat operations (i.e. the military has to be able to brak stuff efficiently and to hand over the pieces to subsequent civilian authority in accordance with the overall, wanted political endstate); and State has been given coordinate authority over phase IV so that the military in principle only has a supportive function - the chief of State's Office for the Coordinator of Reconstruction and Stabilization (S/CRS) is in charge of coordinating this particular element in the inter-agency process (not really sure how it/he formally ties in with the NSC which is in charge of the overall process).
Pre-conflict on the other hand is about identifying and addressing - ultimately managing - emerging conflicts so that they do not evolve into something we cannot live with for humanitarian or security reasons, or both. If we put on the USG glasses then, in principle, this challenge calls for both civilian and security (military and covert) means, because the challenge in itself has a political and anthropological character - it cannot be purely military. Much of the existing framework of international organizations and here especially the UN deals with pre-conflict. Development policy itself is a central piece in this puzzle. Conceiving of development policy as a means in to a pre-conflict management end is controversial but helpful.
Pre-conflict there has not recieved the same institutional attention as post-conflict. Only the JFCOM is developing a new Joint Operating Concept for 'Shaping' operations. The CINC at AFRICOM will be likely to get the responsibility for contingency planning like the other CINCs have. A number of these will be proper war plans. The majority will likely deal with evacuation, humanitarian assistance and especially FID, COIN and counterterrorism - foreign internal defense operations and (support to) counterinsurgency. But the most consequential work, if the AFRICOM commander gets it right, will be based on the conceptual work being done on pre-conflict issues.
There is an institutional trap here: the military traditionally is very strong in war planning. In its self-understanding the military exists to carry out major missions. These are represented in war and contingency plans. But the pre-conflict logic is more civilian, oriented towards day-to-day process of political subjects (but it is at the same time more general, strategic than a war plan case). The challenge for both JFCOM and AFRICOM will be to enhance the pre-conflict stuff to the same institutional importance as those threats that can be addressed through war planning.
The military develops and produces contingency planning and joint concepts at COCOM and JFCOM levels. No such equivalent exists within the civilian apparatus. The US military has some unique institutional strengths in planning and concept development, both in terms of talent and numbers, and in terms of formalization of process. The civilian side could learn a lot from these guys.
But there is an institutional imbalance here. Neither State Department or the NSC have ressources for strategic planning comparable to Pentagon's. Pentagon is 'only' responsible for developing plans and JOCs in support of the overall USG inter-agency process on pre- and post-conflict where the civilian agencies are in the lead. One solution is of course for e.g. the AFRICOM commander to involve or integrate civilian agencies very much up front in strategic planning and forecasting. But even if this is an understandable and pragmatic approach there is something lopsided about a process that will then hinge the institutitional setup of carrying out US foreign policy (State's domain) on the individual character of e.g. the AFRICOM commander. In the end, pre-conflict management can then be boiled down to whether the given commander 'gets' the political and anthropological stuff.
That seems like an unnecessarily contingent element. Maybe State Department or the NSC should get into the conceptual development and planning work on their own account so that they get a better - more strictly institutionalized - chance of getting heard? That might also ensure, that the military winds up with less situations where they are formally in a supportive function while really having to do it all.
* For the non-US reader: the 'inter-agency process' is the term describing the policy coordination going on inside US Government (USG). The National Security Council is the agency responsible for the process concerning national security matters.