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The problem originates here: https://github.com/ros-infrastructure/catkin_pkg/blob/ad07ab2570006a72994657ab3f3267a9e84469aa/src/catkin_pkg/packages.py#L96
It appears that there are duplicate packages in your source directories, which isn't supported. All packages should have unique source directories.
It's difficult to get errors like this to bubble out of EMpy, but this might be grounds for an issue against the catkin package. At the very least, it should be possible to attempt to crawl the packages priory to template expansion to discover errors like this and report more actionable error messages.
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