We have Jira server running in a subdirectory; jira.ourcompany.com/jira
In the application link we configured the Application URL as jira.ourcompany.com/jira
When we use the "Insert JIRA issue/filter" widget, it will show the Jira title etc. However, the link will point to jira.ourcompany.com/project-number instead of jira.ourcompany.com/jira/project-number.