You don't short the battery when you set the jumper to clear CMOS. Otherwise why would they bother putting in a jumper to clear the CMOS if you have to remove the jumper too... especially when removing the battery clears your CMOS irrregardless of what setting your jumper is on? The jumper is the primary way to reset a computer's BIOS, or as seen in many newer computers they just have a momentary contact switch that is effectively the same as using the jumper but a little easier to use (or hit accidently lol).
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