Recently the branch commit links are no longer appearing under the JIRA issue when submitted. The issue key is being referenced in the commit message, but the links are not showing under the ticket.
Please advise.
Are you using a plugin that is reading from the repo? It could be that the connection to the repo is no longer working. It could also be that JIRA hasn't refreshed its info yet.
Commits from where? SVN? Bitbucket server? Check if your Application Links are still working or if your add-on for SVN is still working.
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