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The checkboxes next to file names in the Unstaged and Staged sections of Commit don't do anything in Split View Staging.
In the Unstaged section, checking one used to move its respective file to the Staged section, and likewise unchecking a file in the Staged section would move it to the Unstaged section.
Now the only way to move files between the two sections is to drag and drop, or check the box in the header for the section, which moves all files in that section over.
This began happening after I accidentally clicked "Stage Hunk" from the right-click context menu in the Unstaged section. Now it seems to treat all changes to a file separately, as each hunk has to be staged individually.