basic setup: src and include

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I have a project with a very simple directory layout: .cpp goes to src and headers goes to include. The first problem is that I have to mix libraries configured with a lib-config utility and libraries that have a package file. How can I do this? And the second problem is that I dont know what to put in include/Makefile.am, all tutorials I have found uses a simple src layou with no separate header directory.


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