fix a case where file tracked by git unexpectedly becomes annex pointer file

fix a case where file tracked by git unexpectedly becomes annex pointer file

smudge: When annex.largefiles=anything, files that were already stored in
git, and have not been modified could sometimes be converted to being
stored in the annex. Changes in 7.20191024 made this more of a problem.
This case is now detected and prevented.