I'd like to make a backup of Fisheye and Crucible data, in order to migrate to a different server . Do Crucible backups (made using <Crucible home directory>/bin/fisheyectl.bat) contain the Fisheye data as well, or should I also backup Fisheye data (using <FISHEYE_HOME>/bin/fisheyectl.bat)?
Since Crucible and FishEye run under the same process (they're just licensed separately) your backup will include information from both. If you are backing up using the command line, please just attend to use the --cache argument if you also wish to include the repositories caches (which is basically all the indexed information from your repositories, so you don't have to re-index after restoring your backup).
Also notice that there's an option to create a backup via UI, so you don't necessarily need to use the command line to backup (but for restoring, the only option is by using the command line).
I'd recommend you to check further about Crucible backup at https://confluence.atlassian.com/crucible/backing-up-and-restoring-crucible-data-298977490.html - this document contains all the necessary steps for backing up everything, and subsequently specific details for when restoring a backup.
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