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Some high-end SCM's (including the one we're using at the moment - vesta) require that you do NOT checkin binaries. Eclipse forces you to dump binaries into your project folder. There is no justification given in the docs for WHY eclipse does this, and I cannot think of a rationale for forcing it - why should eclipse think it is cleverer than I, the programmer, and force me not to do an entirely sensible (and, in this case, entirely necessary) thing? The SCM will not let you checkin with a non-source directory of binaries present , unless you check in the entire binaries, and eclipse refuses to behave nicely and just do the decent thing - let the programmer decide where to output to!
Eclipse is simply forcing a linked folder to be within the project, but that linked folder can point whereever you want. So you can create a linked folder to a folder outside the project and you set this linked folder to be the output folder. Does this solve your issue?
Please reopen if linked folders do not solve your problem.