[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2017-04-07T16:24:59Z"
 content="""
The root problem is, you have set annex.largefiles=nothing temporarily when
adding the file. But, when git commit re-smudges the file, that is not set,
so git-annex generates a v6 pointer, which is what gets committed.

I don't think you will have these problems if use use .gitattributes to
configure annex.largefiles.

(There is something going on that I don't quite understand with why
git status then thinks the file has changed. git diff --cached shows a diff
between the pointer that got committed and the actual file contents; 
I would have expected that git would run the smudge/clean filter then and
not show that diff.)
"""]]