Add dirty target safety checks for root instruction shadows

[sjquant]

Why

• tracked root instruction shadows need safety checks before Skul creates or refreshes them
• aborted refreshes must not advance the cached source or delete existing managed files before the safety guard runs

Changes

• add git-index inspection for staged, unstaged, unmerged, missing-HEAD, and incompatible-flag target states
• preflight root-instruction write targets before destructive refresh paths and keep a write-time guard as a backstop
• preview materialization targets so update/apply/add can reject dirty tracked root instruction files before removals
• rollback cached source updates when update aborts after a refresh attempt
• add CLI and git-index regression coverage for refusal paths and update rollback behavior