Largely true, but of questionable relevance to GWOT, which is not fundamentally a fight against insurgents. Our COIN fights in Iraq and Afghanistan are collateral burdens, products of fundamentally flawed (IMO) GWOT policy decisions, not an integral part of the supposed GWOT.
Part of our problem in imposing COIN models, whether FM 3-24 or the Jones model, on GWOT is that it's not essentially a COIN fight: it's not a fight against insurgents. Aside from Iraq and Afghanistan there is no insurgency that requires US intervention in more than a limited FID role, and Iraq and Afghanistan are less the traditional insurgencies that these models are designed to confront (intervention to support an allied government threatened by insurgency) than a natural and inevitable part of the regime change process. The issue is not entirely governance,it's also about foreign intervention.
We may be looking less at a case of flawed models than at a case of models being applied to situations they were not designed to cover.
Certainly causation in this case comes from the Philippine government; I think that's universally recognized. Despite our long-term relationship with the Philippine government, though, these groups have not generally acted against US interests, and have acted against US citizens only in opportunistic situations that are less terrorism than criminality. To the limited extent to which anti-US rhetoric is embraced, it's little more than a nod to groups who occasionally send a little money. It's very difficult to draw any causative line between US policy and terrorist or insurgent activity in the Philippines. Both insurgent groups and their popular base in the Philippines generally approve of us; they see us as a moderating influence on their enemies.
US planners in the Philippines actually did go through a process much like that which you describe. Unfortunately it was very badly done, and considered very few of the factors and influences involved. The outcome was American support for an ill considered "peace process" that was doomed from the start and managed to make things a good deal worse.
One problem with the approach you suggest is that "diplomatic approaches in Manila" are not going to produce any meaningful change. No matter how diplomatic we are (generally not very) we can't make policy for the Philippine government, nor can we persuade or compel the Philippine government to follow our policy recommendations. It's another country, and our influence is not that great.
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