I don't find any indication that magic damage ignores armor in the spell list but then again it makes sense that at least some spells do.
Am I missing something here?
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Magic in its entirety does not ignore Armor but there are some spells with Penetrating Damage which will.
Player's Guide Pg 40 / Core Rulebook Pg 76 : Armor and Shield Details
When you take damage in combat, you subtract the armor rating before losing Health. This applies each time you are hit, so over time, even poor armor can prevent you from taking a lot of damage.
Certain attacks, however, can bypass the effects of armor. They inflict what is called penetrating damage, which ignores armor altogether. Armor offers no protection against penetrating damage.
Player's Guide Pg 50 / Core Rulebook Pg 111 : Spell Format
Description: This entry explains what the spell does in detail. Armor protects against any damage inflicted as normal unless it is noted as penetrating damage (in which case, it ignores armor altogether).