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I don't think you needed to qualify that by saying "for gcc they may not be"; it applies to anything that uses autotools. As long as configure offers the user --bindir, --libdir, and all these other options for freely renaming and re-laying-out the $prefix structure during a configure and build, I think that we need to support them, with a more general approach that will DTRT no matter how the user configures their build.
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