Depends on what you want to delete. Deleting projects is the easiest way to delete the issues and data associated with them. If you have other configuration changes, you will have to delete them separately.
If you want a fresh installation of JIRA without reinstalling, you can...
But, if you want just to delete the issue data but keep the configurations (workflows, users etc), just delete the projects, as Jobin advised.
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I'm always renaming the dbconfig.xml file and deleting the data folder from JIRA Home. A faster alternative that doesn't require JIRA restart is to create an empty backup and restore it every time you need to clean your JIRA instance.
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Thanks John ... Its just that we imported from a bugzilla source and we want to do a fresh import instead of importing on top of what was there. I wasn't quite sure that deleting projects was actually enough.
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