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Familiar with Autotools?

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I've been using the Kyra Sprite Engine, and I am trying to build a custom version of it for my project's distributable. It depends upon SDL and SDL_image, and I created custom versions of those libraries, passing configuration options to them to remove a lot of dependencies. When I configure kyra to build, I pass in some prefixes for my custom versions of the SDL libraries. When kyra builds, it creates two libraries, libkyra and libengine. libkyra builds with the correct SDL libraries, but libengine uses the system installed libraries. I figure that there is a problem with how autotools is configured for this project. It used autotools a few revisions ago, but the current revision is actually a broken build. See the help forum on Sourceforge for more information on what is needed to build it and the issues I am encountering. I would really love some assistance with this problem. Either my understanding of the problem is wrong, or I just don't understand autotools enough to get it to do what I expect it to do. Thanks in advance for your time!

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