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With a pod after 1900, make it so that Indonesia includes the rest of the muslim and other parts but excludes islands to the east.
I am imagining an Indonesia thats limited to the Malay pensula, Sumutra, Java, Borneo, Sulawesi, Bali and a few other small islands. This would mean it gains otl Malaysia, Brunei and Singapore, but looses west papua and much of the Moluccas.
Maybe before independence, Timor, Papua and the other Christian islands become united as a separate state or remain under Dutch control?