Также удостоверьтесь, что Вы тестируете его и в Firefox и в IE. Существуют некоторые противные ошибки с флажками JS, которыми управляют.
The question to which you link: How to automatically remove all .orig files in Mercurial working tree? has an answer that suggests using an update hook to delete the files automatically, which you could very easily turn to a 'mv'. That would be automatic and easy.
I'm not sure that's mercurial doing that, it might just be your merge programs. If it's mercurial, I'm sure it's not currently configurable.