Great link, DD. Thanks for posting that.
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The ulema were uncertain which verses to codify into sharia's worldview. For instance, should they use the one that states there is no coercion in religion (2:256), or the ones that command believers to fight all non-Muslims until they either convert or at least submit to Islam (9:5, 9:29)? To solve this quandary, they developed the doctrine of abrogation – naskh, supported by Quran 2:105. This essentially states that verses "revealed" later in Muhammad's career take precedence over those revealed earlier whenever there is a discrepancy.
Why the contradiction in the first place? The standard answer has been that, because Muhammad and his community were far outnumbered by the infidels in the early years of Islam, a message of peace and co-existence was in order. However, after Muhammad migrated to Medina and grew in military strength and numbers, the militant or intolerant verses were revealed, urging Muslims to go on the offensive.
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Maximum ten years of truce before further expansion is an interesting nugget too. Don't let anyone put all this "into historical context" of the Mecca versus Medina wars since, if that is all it was meant to mean then why did they ever expand out of Arabia? Why all the way across Africa, Spain and as far as Toulouse? Why the Ottoman Empire, the Indian subcontinent and SE Asia?
Sure, peaceful conversion means you can acquire territory without losing your own troops. It's a win:win situation but history tells us there were a lot of battles, even before the Crusades.