Add git index primitives for root instruction shadows

[sjquant]

Why

• root instruction shadow support with the Git index primitives needed for tracked root files
• cover the Git states that later safety checks and shadow lifecycle commands depend on

Changes

• add a new git-index helper for tracked-path detection, HEAD:<path> blob reads, index stage inspection, index flag reads, and skip-worktree toggles
• add integration-style tests for tracked, untracked, missing, staged deletion, unmerged, and skip-worktree scenarios
• fix tracked detection so staged deletions remain classified as tracked while the path still exists in HEAD

Verification

• pnpm exec vitest run src/git-index.test.ts
• pnpm test