I've already a productive version of Bitbucket running. Due to the fact that we had already setup a Stash instance, we've a little bit messy folder structure. It's nothing to worry about but ugly.
Am I able to setup a Bitbucket Server from scratch with the same data (so, without erasing the database)?
Could you please provide further information about how your folder structure looks like? I'm not sure I understand how it got messy.
Either way, please allow me to already suggest something that wouldn't affect your existing instance, so you may test a new install. You may generate a full backup from your existing instance then, in a separate test server, install Bitbucket from scratch and restore this backup to it.
You will find information about Bitbucket backup at https://confluence.atlassian.com/bitbucketserver/data-recovery-and-backups-776640050.html - this documents explains how the backup process works and also presents you with two approaches you can choose to perform it.
First of all an earlier version of Bitbucket failed in recognizing the right "Program Files" folder and created another folder called "Programs". So, we have two folder called "Programs", one of them is the real "Program Files" folder and the other is really called "Programs".
Further down in the Atlassian folder we have three folders called "Bitbucket", "Bitbucket_4.0.2" and Stash. The Bitbucket-Home-Directory is stored in a folder called "StashAppData".
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