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Automatic branch merges only work for one repository

We are using automatic "Branch Updater" merges when building a QA release. We use multiple repositories for the integration. Bamboo only merges one repository to the release branch and there is no option to select the repositories to include in the merge nor a way to add a second Branch Updater for a different repository. Is there a way to have Bamboo merge more than one repository? How do I define which is the master repo?

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