When I create a repository in Bitbucket Jira see's them without any issues. However if I create a repository under a project in BitBucket Jira can not see them.
Hi Jeffrey, are you using Bitbucket Cloud or Server? I've tried reproducing your issue using my Cloud accounts, and I was able to see the repositories under projects in Bitbucket, both in the Development section and in the DVCS accounts menu in JIRA. Keep in mind that projects are created under team accounts so if you want to see all the repos available in the DVCS section, you'll need to add your team by clicking on the Link Bitbucket Cloud account button.
For more information, you can visit Bitbucket projects.
Let us know if you have any questions!
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