The traditional religious clerics and secular authorities amonf the Turkic people in the Tarim Basin (now known as uyghurs) voluntarily joined China. The Qarataghlik Khojas (who were sayyids) wielded religious power and they, and the mullahs, begs, Khana, and the Chagatai prince joined China againat the Dzunghars and their Aqtaghlik puppets.
As long as the traditional authorities and reliigious structure wer in place there was no separatism. The clerics did not promote separatism. There was only traditional Islam. China supported keeping the status quo and the clerics and mullahs and begs in power.
Then pan Turkic jadidists who wanted to modernize and reform Islam came in, spread pan Turkic nationalism and separatist sentiment in Xinjiang. The First East Turkestan Republic separatists were inspired by this racist ideology and promoted Turkic supremacy even against non Turkic muslims. The Hui Muslims then crushed the Uyghur rebels and destroyed the republic.
A second strand of separatism was instigated by the Soviet Union. The soviets created the Uyghur ethnicngroup in 1921 and wrote uyghur nationalist histories and promoted uyghur nationalism and separatism from China. The Uyghur leader of the Second East Turkestan Republic during the Ili Rebellion, Ehmetjan Qasim was a member of the .Soviet communist party. Hui and Salar Muslims in the Chinese army fought against the Soviet backed Uyghur army in the Ili Rebellion.
http://www.defence.pk/forums/europe...-300-muslims-during-prayer-2.html#post4399760
The Soviets supported Uyghur militant separatists especially after the sino soviet split during the cold war.
The separatists running around today, the ETIM are influenced by Al qaeda. They are allied to the TTP and you know their ideology already.
