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The repository settings page should support entering a domain for NTLM authentication. This should be shown optionally since NTLM is less common than standard HTTP auth, e.g. by showing a combo box that requires explicit selection of NTLM.
Mylyn has been restructured, and our issue tracking has moved to GitHub [1]. We are closing ~14K Bugzilla issues to give the new team a fresh start. If you feel that this issue is still relevant, please create a new one on GitHub. [1] https://github.com/orgs/eclipse-mylyn