Sparse checkout (both manual config and git sparse-checkout set) kept
leaking config to the main checkout, hiding .story_kit/work/ and
breaking the IDE. Replace with git update-index --skip-worktree which
marks work files as unchanged without removing them from the worktree.
Files are present (builds work), but changes are invisible to git
(no merge conflicts).
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>