By default FishEye indexes entire repository history, so this is a reason why you can find deleted files and directories. In order to not show particular folder at all, you can exclude it from indexing - see https://confluence.atlassian.com/display/FISHEYE/Include+Exclude+paths. Please note that you will have to reindex the repository after change.
Everything below is tested on Ubuntu 17.10. I prefer to use Jira in a docker container because: 1. I can install Jira with a couple of commands. 2. I can start and stop Jira just by starting and s...
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