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Stefan HallerandClaude Opus 5
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The diff of a deleted file is its content going away, so putting every line of it into the index leaves an empty file there (modified in the index, deleted in the working tree) rather than the deletion the user selected. The reverse case matches: the diff of an added file is its whole content, and taking all of it back out of the index leaves the file tracked and empty rather than untracked again. In the staging view you had to enter such a file deliberately to reach these cases, but stepping through a directory's diff hunk by hunk runs into them routinely. Selecting every change of a file says "this file", so stage or unstage the file itself. This applies to any file, since applying a file's whole diff amounts to the same thing everywhere else. Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>