The key setting in Agile Project is how the solutions detects if an Issue is done or not. Available options are “Issue Done Statuses“ (default) and “Issue Resolution“.
In “Issue Done Statuses“ an issue is marked as done in its last transition to a status marked as “Done Status“. All Jira status can have three different colors (blue - todo), (yellow - in progress) and (done - green). The default “Done Statuses” are green ones but this is fully configurable dragging the statuses between the boxes below.