fix(cli): clear GIT_DIR in staged divergence check for linked worktrees

[skoshx]

Root cause

When GIT_DIR is set (as git exports it automatically in hooks from linked worktrees), git status resolves paths incorrectly, causing false divergence reports that block --staged scans.

The issue reproduces in any linked worktree (git worktree add) when GIT_DIR points to .git/worktrees/<name> rather than a real .git directory. Git exports this variable to all hook invocations, so it affects every pre-commit hook run from a linked worktree.

Scope

Applied the same GIT_DIR: undefined fix from #1516 (which cleared it for scoped scans in core/services/git.ts) to runGitRaw in cli/utils/git-hook-shared.ts, which is used by the staged divergence check (findStagedSnapshotDivergences).

The fix:

• Only affects the --staged divergence check path
• Does not change any diagnostic logic or output
• Mirrors the existing worktree fix in core

Testing

Added a regression test in find-staged-snapshot-divergences.test.ts that:

1. Creates a linked worktree
2. Stages a file
3. Sets GIT_DIR (as git would in a hook)
4. Verifies the divergence check returns an empty array (no false positives)

All existing tests pass, including:

• ✅ React Doctor CI (100/100, 0 errors, 0 warnings)
• ✅ All platform tests (Ubuntu 20/22/24/25/26, macOS, Windows)
• ✅ Lint, typecheck, CodeQL

Parity

Expected: zero diagnostic changes, as this fix only affects environment setup for git commands (clearing GIT_DIR before running git status).

The React Doctor CI scan confirms no new diagnostics were introduced. Full corpus parity can be validated if needed, but given the focused nature of the fix (identical to #1516's approach), diagnostic regressions are not expected.

Closes #1630

  

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commit: 92c65f3

[github-actions]

React Doctor found no new issues. 🎉

_{Reviewed by React Doctor for commit 92c65f3.}

[github-actions]

Interactive terminal E2E

Terminal Control verified the built CLI at 92c65f3 in a real PTY:

• selected a project interactively and observed Scanning... before the three-second Git delay completed
• waited for the clean result and exercised the compact report
• opened copy context and the GitHub Actions confirmation, then cancelled safely

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