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You may add new entries to existing encounter tables by including encountertablesEncounterTables.xml in your mod, using an existing table name and setting the Load="Merge" property on the encountertable tag.

<?xml version="1.0" encoding="utf-8"?>
<encountertables>
  <encountertable Name="Ammo 1" Load="Merge">
    <objects>
      <object Chance="100" Number="3d6" Blueprint="My New Ammo"></object>
    </objects>
  </encountertable>
</encountertables>

Adding and Replacing Population Tables

You may add new population tables and replace old ones by including PopulationTables.xml in your mod.

<?xml version="1.0" encoding="utf-8"?>
<populations>
  <population Name="MyMods_SmallGunAssortment">
    <group Style="pickeach">
      <object Blueprint="Borderlands Revolver" Number="1-3"></object>
      <object Blueprint="Semi-Automatic Pistol" Number="0-2"></object>
      <object Blueprint="Chain Pistol" Number="0-1"></object>
    </group>
  </population>
</populations>

Additional Info

Here's a thread on Steam where I discuss using encounter and population tables: http://steamcommunity.com/app/333640/discussions/3/358415738194955181/