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Eclipse and code directory/folder structure

Eclipse apparently requires (or required) a fixed directory structure [the mailing list rant, the bug report, the project proposal]. There is a short tutorial on setting up projects to pull in existing files from arbitrary locations [here, basically File->New->File click advanced]. In a recent version of eclipse 3.3.2 you can specify any root for the project, but your files have to all be under that root.
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