OK, JIRA appears to be a special plugin that gets installed in Netbeans' installation directory which you had dutifully installed as root. So I'll run Netbeans with sudo and all will be well, indeed the JIRA plugin will install...
...at that point all hell breaks loose! When you run it again without sudo Netbeans either fails to start of complains about permissions left, right and centre.
- You've are running Netbeans in your home account as root!
- Your local ~/.netbeans/8.x configuration will be be owned by root
- The ~/.cache/netbeans storage will be owned by root
- Any projects that were open and autocopy their files to another location will have been written as root
Don't ever run Netbeans with sudo!
All the permissions can be fixed but it is a right PITA if you don't know about them all. Instead run Netbeans from root's home directory as root. Simply:
> sudo su -
> netbeans
and then install the JIRA plugin. When you go back to your own account though JIRA might not be listed as an installed plugin it will be listed as Task Repository Connector.
