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What (clone) ranks in the Grand Army of the Republic outrank Jedi Commanders and Generals?

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Most certainly none.

One commonly mentioned point in debates about the Grand Army of the Republic is this: It is not a weapon of war, nor a defensive mechanism. The primary purpose and function of the GAR, like the droid armies of the CIS, is to complete the Sith's revenge of exterminating the Jedi Order and complete galactic conquest. As such, the aim is to spread the Jedi thin across the galaxy, use the war and its battles to distract them from the encroaching dark side and to feed the arrogance that has seeped into their ranks, and earn their absolute trust as fellow comrades, so as to set up the perfect opportunity to strike them all down with one executive order.

That is why the clone armies "ordered by Master Sifo-Dyas" placed the Jedi Order at the head of its field command, so that as many of them will be sent out to lead the charge on the battlefield across the one million contested worlds of the Clone Wars as possible. There may have been non-clones on equal or lower rank - such as Captain and later Admiral Wilhuff Tarkin - but none superseding the Jedi, as per Palpatine's intent.

But we all know it's an act. Officially, the Jedi are the highest ranking field officers, with Supreme Chancellor Palpatine and the Senate at his feet being the sole overriding authority. In truth, the clone commanders are the ones in charge. Deferring to the Jedi is an elaborate act - for what is the rank of Jedi General - even Padawans are Commanders - if not for painting targets?

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