Multiple different configured projects in one dir

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I have a autotools build which generates a few binaries - and one being a sort of compiler - so I'd probably need to configure this one binary with the --target parameter.
My questions are:
Do I need 2 seperated builds to achieve this or can I change the target for one binary in particular. When I need 2 builds - is there a way to link them together (to ease configuration/compilation)?


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