The standard argument here is that the project requires all contributors to sign some form of document granting rights to the project. The project uses JIRA's permissions to whitelist people who have signed the doc.

i.e. in Clojure's case, the Contributor Agreement grants copyright to the submitter AND Rich Hickey, so he can change the project's license in the future, if need be.

It seems like Github should add this feature, (open source, with whitelisted contributors) and then the need for the JIRA mess all goes away.