Customisation that can't be done with add-ons and direct database reporting (which is a stupid and horrible idea because the database is not in the slightest designed for it and is the single worst possible way to report on Jira and Confluence)
In a Server deployment of Atlassian's products, you control the application. In Atlassian Cloud, Atlassian controls all aspects of this and manages it for you.
But in Server, you are responsible for managing your own equipment, performing upgrades, etc. The major benefit to server is that you have total control over your data in a Server deployment. With direct access to the files and the database, you could make changes to your data circumventing Jira entirely in the process if you wanted to.
Many admins never need this level of control. However others can use this for manipulating their data, troubleshooting problems with Jira, or in some cases, even modifying the Jira interface and layout.
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