The way I usually generate .EMP files is:
1) Start a random game, max AIs, no Neutrals.
2) On turn one, set all AIs to human control.
3) As each AI takes its turn, "Save Empire"
If the AIs were patched by my patcher, that is the end of it. If not, then:
4) Start a new game, "Add Existing Empire", then edit and add the required normal/civilized/etc. traits.
5) Save Empire again.
It goes pretty fast that way.
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