Путеводитель по Руководству Linux

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   git-update-index    ( 1 )

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       where the stat entry is out of date.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.