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SI: Evocation/Necromancy doesn't protect you against your own damaging spells.
Some spells are indeed affected, however. It does make you immune to your own webs, but fireballs, incendiary clouds, meteor swarms, skull traps (SI: Necromancy) affect you normally.
I only tested a bunch of spells of those two schools, but I'm guessing it's not supposed to happen.