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Modify upgrade effect

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Most upgrades simply are set as requirements to unit/building creation or have their effect set in the data of the upgrade itself (it then applies on all units that have that upgrade in used upgrades).

However what I understand from your question is how to increase the effectiveness of a certain armor type.
This can be done in the Gameplay Constants where you can find a table of real values which are factors of the damage taken from the attack type to the armor type.
 
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