I already know the documentation at https://confluence.atlassian.com/display/FISHEYE/Git and I was able to add several repositories we have at github.
However is there a way to include (selected) forks?
FishEye allows you to add the fork of a repository as a separate repository. This will allow you to index the fork, but unfortunately FishEye does not have any mechanism for recognising commits shared between repositories. So any commits that exist in both the forked and original repo will show up multiple times.
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