I searched for the answer to this question but couldn\'t find any good. Maybe they\'re old and something has changed, so I ask again.
I have a directory structure as
Automake doesn't cope very well if you try to set up your directories in a different way than it expects. What you want would involve writing extra rules to move the binaries to ../bin after compiling them, which is needlessly complicated.
If you don't want to clutter your source directory, try this:
cd my_project
mkdir build
cd build
../configure
make
That will put all the generated files (like makefiles, binaries, object files) in subdirectories of my_project/build.