I'd strongly advise against using symlinked folders any more (or even seperate whole installations).
The most recent changes to how WoW updates itself do not play well at all with symlinked installs, namely the downloading of content while in game, that cannot be disabled by running wow.exe without launcher.exe, and the locking of files to prevent them being written while one of the clients is modifying them. I've had numerous crashes shortly after updates, which I could only fix by deleting the files mentioned in the crash reports, and having them download all over again. Repair.exe of course says nothing is wrong, even with 3GB data files missing. Having to run the launcher from each individual folder kind of defeats the purpose of having a common set of folders for each install.
The wow client also updates the registry every time it's run, modifying the program's location to the location it was last run from. This affects programs like WoW Model Viewer and the Wowhead client.
There isn't even any need to clone folders any more. The only reason I was doing it was because there weren't enough macros available per character, until I could give each one the use of all the per-account macros too.
Addons (like Jamba, or the addon part of ISBoxer, which is configured from the main program) will give you all the macros you need, without taking up any of the normal character or account macro slots.
If you want to have a seperate config.wtf file for each character, you can do that without having to maintain seperate folders, simply by having a powershell script build or swap it in before launching WoW (if you're using HKN. ISBoxer has this built in).
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