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Yeah, all his arguments are true for most bugtrackers.

By Jira he seems to really mean 'Jira at Apache' - which is their bugtracker for most projects.

I think the OP is referring to the Apache Foundation's process for accepting patches from non-committers. All Apache projects require a copyright grant. The only way (AFAIK) that they allow you to express that you grant the copyright for your changes to the foundation is by checking a box when you upload the patch to their issue tracking system, which happens to be JIRA.

Specifically the problem is uploading text patches to JIRA, as compared to doing pull requests on github.