Our phabricator is install at http://www.mysite.com:8080. In the new version of the repositoy UI, the clone URL of my repo now shows http://www.mysite.com/diffusion/RP/repository/, which should be http://www.mysite.com:8080/diffusion/RP/repository/.
Note the actual repo URL with 8080 is fine. We can clone/push/pull successully. It's just the URL shown in Diffusion UI is not correct.
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This should be fixed in HEAD of master. Thanks for the report! Let us know if you run into anything else.