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The Agile Project/Issue Management blog by Chris gives Jira a thumbs up as a “fantastic traditional bug tracker,” but it apparently falls short for agile development.
There are folks who use Jira for agile development and a number of resources you (and others) might want to take a look at.

• Read how we use Jira for agile development in our developer blogs
• Using Jira in an Agile Environment includes two Jira plugins that may be of interest
• Agile developers can find more discussion of Jira — pros and cons — for agile development in our forums.

Thanks for the feedback!