Since Atlassian recommends to use native database backup tools for regular backups, which tools can be used with SQL Server 2008? Do i need to configure these tools with JIRA? Is there some plugin available for back up in JIRA?
What they are referring to is that you should back up your database with whatever tools the vendor recommends for backing it up.
Jira's data lives in the database. If you have that database running on MS-SQL Server 2008, then you should back up that data using MS-SQL backup tools (Although you'll need a copy of the attachments directory from the JIRA server, and I'd recommend a backup of the installation, but those are all simple "copy file" processes)
You don't need any plugins - all your backups should be done outside the tool.
However, project backups are a different story. The answer is that you really need a backup of everything, then you can extract individual projects as needed. You should use JIRA's xml export to create the backup - another JIRA can read that for individual projects.
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