Can we load a different application within JIRA window. Meaning I will have a link on JIRA menu bar for our inhouse application and I wanted to access the application within the same window.
You could write a simple plugin with a web fragment that adds into the menu bar (like Agile, Portfolio and other plugins do) - see https://developer.atlassian.com/display/JIRADEV/Tutorial+-+Adding+menu+items+to+JIRA
Or add it as a link on the "hamburger" menu dropdown - Admin -> Application manager
Ah, no, that's not how they work. Agile, Portfolio and so-on are NOT applications. They are *Addons* which you add to JIRA, and run entirely inside it. You cannot install them separately, they live and run inside Jira. If you want your application to run like them, then you will need to rewrite it as a Jira addon.
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