We currently have smart commits enabled in fisheye and we have 6 repositories. I want to add a new repository but I don't want smart commits for this one. This question: https://answers.atlassian.com/questions/133538/when-merging-from-forked-repositories-git-commit-messages-are-imported-multiple-times-how-do-i-deal-with-this seems to indicate that you can disable smart commits for a specific repository but I can't find that anywhere in the UI. I'm running Version:2.10.3 Build:20130318234358 2013-03-19.
the question you've linked seems to relate to the JIRA DVCS Connector.
FishEye doesn't currently support disabling smart commits for specific repositories.
https://jira.atlassian.com/browse/FE-4301 is probably the issue you should vote on. Be sure to leave a comment about your specific use case, if it's different from the one described in the issue.
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