I don't know if you are a developer, but it might be possible that you still
have have queue in one of your repositories. To test this do
sage -hg qdiff
in the different repositories.
Also did you try removing (or beter moving outside the sage directory) the
not tracked file somewhere?
Also can you give the output of the command:
whoami
and
ls -l /usr/local/sage-4.7/local/bin/.hg/
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