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This error is caused by the discontinued Atlassian's plugin Subversion for Jira. It has a bug and the service is not removed along with the app and it remains active causing errors. It must be manually removed from the Jira administration services section and reboot Jira.

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Negotiate authentication failed (on Windows) 

Try by configuring the order to negotiate authentication by adding the following property to the JVM configuration and re-starting Jira:

-Dsvnkit.http.methods=Basic,Digest,Negotiate,NTLM

Please, read this Atlassian's documentation for how to add the property above to  your Jira instance configuration startup:

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