Autoconf and doxygen outside source directory

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Hello;

I need to include doxygen into a autoconf / automake project. Here is my problem. The problem is this project uses a fresh build directory outside the source. You call the configure outside to set up the files and compile. I need to get doxygen to scan the source folder and run doxygen and then make the html outputs.

How do I tell doxygen where the source folder is and then get it to work on those files and then output to the new source folder?

Thanks,

Dave

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