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Call To Power 2 Cradle 3+ mod in progress: https://apolyton.net/forum/other-games/call-to-power-2/ctp2-creation/9437883-making-cradle-3-fully-compatible-with-the-apolyton-edition
In the data folder, there's a file called UnitRules.xml
Important: Be sure to take backup of the file, before editing it
Just open it in notepad, and try to find the spy
I don't know if you can just delete it, or maybe try to change some of the things, so it has no powers or something... I haven't tried it myself...
"I've lived too long with pain. I won't know who I am without it. We have to leave this place, I am almost happy here."
- Ender, from Ender's Game by Orson Scott Card
If you want to do it for multiplayer, I think the only way to do that would be to modify the 'Tribe Mask' for the unit type you wish to disable. The mask is a simple binary entry with each position coresponding to a nation type.
With some deduction, you can figure out what each position is by looking at units that are exclusive to that nation. i.e. Eagle Fighter is only for the Bantu, thus it's mask is something like 00000000000001000. Not sure on the number of leading zeros but the Bantu are the fourth position from the right.
Thus to disable spies for all nations, you would set the mask to all zeros, just make sure you have the proper number of digits.
Of course, everyone in the multiplayer game would have to have the same unitrules.xml file.
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