I have no doubt that Ramzi Youssef's Manila group was in direct and constant contact with Pakistan and Saudi Arabia, and that there was input from both directions in the plot. His involvement with extremist groups in the Philippines has been widely overstated. Most evidence suggests that while he was in regular contact with Khalid Sheik Mohammed, he avoided most contact with local groups in both Manila and Mindanao for security reasons. This of course was wise: ASG was host to known police assets and the Muslim underground in Manila is riddled with informers. I don't think anyone in ASG would have been privy to the details of the plot.
A great deal has been made of the fact that Youssef claimed the JAL bombing for the ASG, but I suspect that this was done mainly to put KSM's project on the map and divert attention from him... he obviously wouldn't want to announce his presence in Manila.
Despite his security concerns, I've some reason to believe that the group was not "compromised" in the manner that was widely reported, but that's another story!
That concern was very much with us after the Superferry bombing, but the RSM never got back on its feet after the arrest of Ahmed Santos and subsequent attempts to harness the potential of the Balik Islam group have not produced much result. The potential is certainly there, but the extent to which it's a major concern remains open to doubt. We'll see.
The suppression is only half the story. The decline in sectarian violence in Sulawesi and Maluku has had an impact as well. Those incidents got a lot of attention and were spun as violence against Muslims within Indonesia (not endorsing that spin, but it was there), which was enabler for groups like Laskar Jihad, which recruited Muslims to support their local brethren. That in turn served as a jihadi recruitment pool. The decline in that violence has diminished public attachment to radical causes and affected recruitment, fundraising, and willingness to give shelter and passive support (i.e. not informing). JI's habit of attacking soft targets that include many Indonesian Muslim casualties hasn't helped either.
Suppression has played a part, but the environment overall is not that conducive to replacement of the people removed from the movement or to the spread of radicalism outside the inner circle.
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