if you go to windows -> preferences -> pydev -> interpreter, you can configure the pythonpath variable used by python under eclipse, and add whatever project directories you want so that they are visible when executing python inside of eclipse.
i find it easier to execute my code outside of eclipse and use better system tools for the pythonpath. and for that matter, just use emacs or vim.
in general, though, you don't want to mess with the eclipse settings that describe the workspace directory. it's better to just append project code locations to the eclipse/pydev pythonpath.
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