Problem is that repositories under organization are not visible after linking github to jira. I have created organization level oauth-tokens and I have administrator rights for the organization in github. After linking them jira asks for my github password but there is “no repositories” after I log in.
currently Github Importer allows you to only selected your own repositories or 'starred' ones. So currently you'll need to manually 'star' a repository before starting an import.
We are aware that it's really annoying and we have an improvement request for that: https://ecosystem.atlassian.net/browse/JIM-1410. I'll try to squeeze it to my current sprint, so a fixed version of importer should be available on Marketplace within a week.
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