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Haha, well it is Easter after all.
Funnily enough in my Eclipse setup I have done exactly what you suggested and put all my plugins within that source control exempted "plugins" folder. And that got me (usually) the behaviour I wanted. Well until it stopped working on a bunch of files for no obvious reason I can see.
It was actually user_none who suggested that it should be possible to have the plugins in a separate folder and do something with external libraries, so I set it up that way in anticipation.
In the meantime I still have my "Eclipse" copy of the tree/setup to use - but as John reckoned the pydev stuff came from the aptana guys that he had less issues with that setup so I figured it was worth trying...
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