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I work with people who have created a (CVS) source directory structure where one entry on the classpath is a subdirectory of another -- e.g., CLASSPATH=a:a/b/c Eclipse does not allow me to have two subdirectories on the source build path, despite that the fact that (quoting colleague) "it works for me with emacs and ant!". And, in fact, it will usually work, though there are some in-theory-this- will-fail scenarios that this sort of classpath enables. My workaround, for now, is to ignore all the files that fail to compile because they reference classes found in the forbidden directories. I have no objection to Eclipse making all sorts of insulting remarks when someone tries to do this, as long as it is at least allowed -- in my experience, it is easier to fix software than it is to convince someone else that they have made a mistake.
We want to allow nesting source folders (when excluding the nested one from the enclosing one). This is on the plan for M4.
*** This bug has been marked as a duplicate of 25928 ***