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As a follow up, I thought I had a circular dependency in my packages because when i call rosmake with a few of my stacks, i see this message:

[rospack] woah! expanding the dependency tree made it blow up.

But when I manually created a circular dependency in some packages, they would not even compile. Because rosmake found the circular dependency right away. Even if I tried to compile with the "-s" flag.
Maybe that message is only for inter-stack circular dependencies? But rosmake seems to handle it fine, so i am not worried about it.