We have local instances of JIRA Agile and FishEye/Crucible. For our source code we have a single repository that hosts many projects. I initially setup FishEye with just a single repository and set relative paths in the FishEye configuration. This seems to mess up things because both FishEye and Crucible also watch the root level.
So I removed the single repository and replaced it with a relative repository per project. However this still does not fix the issue, some projects have unrelated commits in the source tab, other projects no commits.
Commits are related to JIRA issues via the convention of adding an issue key in the commit message.
When JIRA renders the Commits tab for an issue, it asks FishEye for all commits containing the issue key of the issue, across all repositories in FishEye. You can use Project Links in JIRA to restrict the search in FishEye to a specific repository however.
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