Autoconf and doxygen outside source directory

[dave]

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