Once the FishEye Confluence documentation is made public, please move http://confluence.atlassian.com/display/DEV/Improve+FishEye+Scan+Performance into that space and update the links accordingly. The 'per-repository permissions' and 'multiple scan threads' problems are feature requests in the old FishEye issue tracker, so if the issues are ported to JIRA by the time the FishEye doco becomes public, please link those to the relevant requests as well.