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Unfortunately, you didn't say anything about the ROS version you are using in your question.

If you are using Fuerte and installed rosdep with pip, rules are not kept in local rosdep.yaml files anymore but in a github repository. Have a look at this page for more information.

If you are still on Electric and your package is in a stack, then you need to put the rosdep.yaml file right next to the stack.xml file. See this page for more information. It explicitly states that you can only put the rosdep.yaml file in a package if it is not part of a stack.