The weakness of using two independent build system probably is not too obvious. However, when you start trying to build the whole project outside of the root directory of the source code, the build will fail. With GNU autotools itself, the build will be successful. Then how do you migrate from Qt build system to GNU autotools? It's simple, use Autotroll (http://tsunanet.net/autotroll/). Autotroll is a set of m4 file and makefile which will help you carry-out what qmake do. This way, the build system will be unified into GNU autotools build system. No more calls to qmake manually (or within a script you made).
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