How do I fix "This Visualforce page is deprecated in favor of a new and much improved JiraIssuesCasePage"?
Answer:
Upon upgrading Salesforce package from version 1.3 or older, the JIRA Issues Page (OverviewPanel) may display the info message. This is due to a deliberate change in the package which requires Salesforce administrators to update to a new Visualforce page available in version 1.4 and newer.
To use the new Visualforce page:
Edit the page layout.
Remove the JIRA Issues Page (OverviewPanel) from the layout.
Under the Case Layout panel, scroll through until you find Visualforce Pages.
Now click and drag JIRA Issues to desired location.
Then, click Save.