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Here is the problem. I did source devel/setup.bash and it sets $ROS_PACKAGE_PATH to the root of build directory. Now when I do rosrun using_markers points_and_lines I have the error of rospack complaining it cannot find these packages. [..]

This is only a partial answer, but the reason is most likely the fact that rospack will only consider directories 'packages' if there is a package.xml in them. In your tree output, I don't see a manifest anywhere.

I'm not sure why this is. You could try and see whether a make install from your build directory results in something different.

Perhaps @Dirk Thomas can chime in?

Here is the problem. I did source devel/setup.bash and it sets $ROS_PACKAGE_PATH to the root of build directory. Now when I do rosrun using_markers points_and_lines I have the error of rospack complaining it cannot find these packages. [..]

This is only a partial answer, but the reason is most likely the fact that rospack will only consider directories 'packages' if there is a package.xml in them. In your tree output, I don't see a manifest anywhere.

I'm not sure why this is. You could try and see whether a make install from your build directory results in something different.different (make sure to set DESTDIR to something valid).

Perhaps @Dirk Thomas can chime in?