After a terrible decision by Atlassian to discontinue the Eclipse Connector for Jira, it seems to me like there is no way to use Mylyn in Eclipse Neon to integrate with Jira. Is
I have not fought with Neon yet, but in Mars which is also not officially supported, I was able to get Jira partly working using this install URL:
Atlassian Connector for Eclipse 3.7 and later - http://update.atlassian.com/atlassian-eclipse-plugin/rest/e3.7
It allows me to see my task list, select Jiras and it will remember working sets for each Jira I select, but one important feature to me I cannot get to work is on the Team Synchronizing perspective I CANNOT add changed files to a change set tied to the Jira like I can in Luna.
I can see incoming changes by jira tied change sets, but not create out going jira tied change sets.
I have broken my Mars install many times trying to update Mylyn but if I take the 3.20 version it foo-bars my install.