Function detectWorktreeIndexMismatch

src/sync/worktree.ts:93–123

(
  startPath: string,
  indexRoot: string,
)

 *     and monorepo-subdir layouts from producing false warnings.
 */
export function detectWorktreeIndexMismatch(
  startPath: string,
  indexRoot: string,
): WorktreeIndexMismatch | null {
  const worktreeRoot = gitWorktreeRoot(startPath);
  if (!worktreeRoot) return null;

  const resolvedIndexRoot = realpath(indexRoot);
  if (worktreeRoot === resolvedIndexRoot) return null;

  // Only flag it when the index root is itself a real working-tree root. This
  // distinguishes "borrowed another worktree's index" from "index sits in a
  // plain ancestor directory", and avoids warning outside git entirely.
  if (gitWorktreeRoot(resolvedIndexRoot) !== resolvedIndexRoot) return null;

  // Don't flag a nested repo (submodule / embedded clone) that `indexRoot`'s
  // index ALREADY covers: indexing a super-repo descends into its submodules
  // and gitlinked clones, so a query run from inside one resolves up to the
  // parent index — whose graph *does* contain that nested repo's files. The
  // warning's premise ("results are a different branch; symbols changed only
  // here are missing") is false there, and its "run codegraph init -i" advice
  // would needlessly fragment the unified workspace index. A genuine borrowed
  // worktree and the index root are the SAME repository (they share a git
  // common dir); a submodule/embedded clone is a DIFFERENT repository and does
  // not — so suppress only when the two clearly differ. (#1031, #1033)
  const worktreeCommon = gitCommonDir(worktreeRoot);
  const indexCommon = gitCommonDir(resolvedIndexRoot);
  if (worktreeCommon && indexCommon && worktreeCommon !== indexCommon) return null;

  return { worktreeRoot, indexRoot: resolvedIndexRoot };
}

/** One-line-per-fact warning describing a detected mismatch. */
export function worktreeMismatchWarning(m: WorktreeIndexMismatch): string {