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East Timor? Phillipines? India? Russia? You cant deny the fact that most religious strife going on in the world today somehow involve muslims.
East Timor had zero to do with religion. It was a right wing military dictatorship (we supported BTW not only the right wing military government but the invasion itself) worried that it would have a border with a possibly radical left wing nation. And the chief planner behind the invasion, was a catholic. At the time most of Timor's population was not even catholic.
The Philippines came from years of forcing Moros off their land, making laws preventing them from ownership of land, bullying them and yes killing them and then demanding the Moros turn over any weapons they have to a dictator. Years of bad policies aimed at the Moros caused what we see now.
Russia and Chechnya started off as Chechnya wishing to break away from Russia.
India, a Pakistani land grab and attempt to bleed them.