In the site's Downloads section you'll find a link to 1.04 reference data, download that and use notepad to edit the appropriate files. The ones for ships are:
CAPITALSHIP_xxxxx.entity
Frigatexxxxx.entity
For example, CAPITALSHIP_TECHBATTLESHIP.entity is the Kol, and FrigateTechLongRange.entity is the Javelis LRM. Tech = TEC, Phase = Vasari, Psi = Advent, those are the internal code names for the races.
The line you're looking for in each ship entity file is right on top:
autoJoinFleetDefault TRUE
Set it to FALSE, and you're good. Make sure to create the mod folder properly, and all that
If you want to do this with an existing mod, if the mod's author left the files in text you can just edit those, and it won't conflict with anything else the mod tries to do.
