зарегистрируйте содержимое файла в рабочем дереве в индекс (Register file contents in the working tree to the index)
USING --REFRESH
--refresh
does not calculate a new sha1 file or bring the index
up to date for mode/content changes. But what it does
do is to
"re-match" the stat information of a file with the index, so that
you can refresh the index for a file that hasn't been changed but
where the stat entry is out of date.
For example, you'd want to do this after doing a git read-tree,
to link up the stat index details with the proper files.