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This is likely due to something specific with my setup and environment, but I figured I'd throw it on here in case anyone has any ideas. The issue seems to be that fisheye is reindexing old commits over and over again for seemingly no reason. I noticed this in 2 ways:
We obviously have both Crucible and Fisheye and we have it connected to multiple Git repositories.
This was a bug relating to when certain internal events were fired and can occur when merging branches within git. This should be fix in the latest version of FishEye 2.7.x (currently 2.7.4).
Which version of FishEye are you experiencing this on? If you are on 2.7.4 I would suggest contacting support.atlassian.com so we can investigate further