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I think it's best to have one repository per stack. To have all repositories indexed, you can provide a rosinstall file that contains all your repositories. This rosinstall file needs to be accessible by a URL, i.e. it's not really necessary to have it in a repository. I like to have it under version control though. For each run, the indexer reads this rosinstall file, i.e. when you change it, the indexer will use the updated file.