Australia and Indonesia both have to keep working damn hard on their counter-terrorism capabilities. The Indonesian's have come a fair way in the past 18 months since back when they denied the existence and capabilities of JI. For Australia also, terrorism was a peripheral interest prior to September 11. Going to take a few years for both countries to see results on the ground.
In the meantime, you have to engage with Indonesia's moderates; the folks who were just as pissed as we were when they saw their contrymen killed on their TVs.
I wonder if any Australian politicians will lash out at Indonesia for political gain? It's possible - I mean, the latest news is they knew via SMS of a pending attack on a western embassy 45 minutes prior to the blast. There were demands for the release of JIs Abu Bakar Bashir. So they didn't "cave in" to the terrorists' demands and I assume there was intelligence sharing - but still, you can see the possibility for backlash.
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