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When you go to "external" mode for Ace addons, the Libraries are put as stand-alone versions and are being loaded just like normal addons. Clever updaters (and jwowupdater is not the only one that can do this) see that and remove the libraries that are included with addons).
If they would not do this what would happen is this: A library gets loaded and registers itself. This may have been happening as part of a non-externalized Addon or by the Library being loaded as standalone library.
Each addon that is externalized will get this library and not try to load it again.
Each addon that is non-externalized has the addon included in its directory structure and referenced. The game's lua interpreter will seek and find the code, compile it and run it. The library code just processed starts to run, notices that the library is already loaded quits. You now have a bit of overhead because the game loaded duplicate code that didn't do anything.
So what you gain by externalizing is a little bit of loading time speedup. It's the more valuable the more ace addons you use.
What is bad in any case is mix and match arbitrarily. An old addon copied into your interface folder may wreak havoc, if it includes a way older library that gets load first. A subsequent addon may then load a newer library which will replace the older one, but that may break the old addon horribly which expects the old library. The point is, either externalize all your ace addons or none. Then chances of something breaking should be minimal.
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