The magic is in the --patch argument to git-add(1). This instructs Git to display all changes to the files specified on a hunk-by-hunk basis and lets you choose one of the following options for each hunk
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In this case, I staged (y) about half of the hunks (the ones that were bookmark related) and left the other hunks unstaged (n). Now my index has all of the changes to synchronize-bookmarks plus half of the changes made to models.rb.