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Little behind but I've forwarded this post to Tupolov who did all the civ work this update.
Any info or help to combat this issue would be amazing.
Log a ticket on our Github so it doesn't get lost. This should be a priority fix.
VCOM shouldn't result in any save/load time increases beyond standard compilation of mod functions, which is minimal.
I haven't seen it done before.
You would also need to check to see if a profile already exists for the hovered group.
Our task system can be finicky, and sometimes just broken. We apologize for any inconsistencies.
Profiling it by syncing it to the Virtual AI Module would persist it. Otherwise you can use custom save/load functions and manually persist it: http://alivemod.com/wiki/index.php/Persistence#Persistence_Script_Commands
Vehicle damage is persisted through save/load but it's a less precise form of damage (number 0-1 instead of specific parts). So if a vehicle is missing a wheel, it will likely get that wheel back. But if a vehicle sustains heavy body damage, it will load with that damage still present.
You need to make sure the pbo's are named differently. On top of that, inside each PBO is a
$PBOPREFIX$ file, open that with notepad and make sure the path matches the name of the pbo it resides within.
I think it works organically just like creating factions with any other sides, all you'll have to do though is create the faction and add units to it. No groups will be needed.
We are always accepting of pull requests if you'd like to add features to ALiVE. Our issue list is not a list of things that will 100% be added. At the end of the day we are all spending our free time working on this mod for no pay, and thus the amount of time we invest will be spent accordingly.