Actually in JIRA 7, the Agile and Service Desk are not plugins anymore. You can consider the following:
JIRA Core: Just JIRA
JIRA for Software: JIRA + JIRA Agile
JIRA Service Desk: JIRA + JIRA Service Desk
And you can manage these applications in the following navigation path (For JIRA 7): JIRA Administration > Applications
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