Choosing between BI and Rome will require a restart of the exe. They use seperate unit databases, building databases, and so on.
The '-mod' command line option has been hugely improved, and should now allow you to keep all your mod-specific data files in a data folder under the mod name, which will also be used to create a folder. Essentially when the game looks for files it will look here first, then for any files it cannot find there it will revert to the original Rome project directory. The game will also place assocated savegames, replays and so on in a directory structure inside the mod folder. BI works much the same way, creating a BI folder which contains the following directory structure:
bi/custom
bi/data
bi/preferences
bi/presets
bi/saves
The BI exe uses this as the default project mod directory, only reverting out to rome data when it can't find what it needs. Anyway, you'll be able to pick it apart soon enough and see what makes it tick...
Hopefully all mods will then be able to do the "right thing" and create a directory structure like this and put a shortcut next to the main exe which is used to play the mod, and starts up the game with -mod:mod_name on the command line...
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