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I use four linked WoW folders but within those folders I went ahead and linked the accounts in WTF/Account. Now, I only have to do one profile in Trinity2, for example, and it's there for all my accounts without having to copy/paste. I've only been doing this for a couple of weeks but I haven't noticed any problems. Is anyone else doing this and have you tried linking character folders as well?
You might have an issue if you don't want all folders to be exactly the same (different character or account macro's, for instance).
This way you can't do round robin casts (each character takes a turn to do a certain task), so it's not an option for me. I'm using symbolic links for:
\Data
\Interface
\WTF\Accounts
\Errors
I'm not sure why you wouldn't be able to do character specific macros. Yes, the global macros are shared (which you want because you will share some macros between the clones), but the character specific ones are still going to be unique per character.
The problem is that anything that shares data per account (i.e., all the stuff that you care about when you do this) will cause conflicts. For me Bongos2 was the dealbreaker. I was driving myself insane trying to remember which toon I had to log off of last so my changes would persist. The global macros have the same problem.