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Git runs hooks from the top of the work tree, so a hook running a bare `codegraph sync` never reached a sub-project's index. Each hook block now names the project root it syncs, shell-quoted, one block per root, placed right after the shebang so a user hook that ends in exit cannot skip it. A hook in another language is left untouched and reported, and a block from an older install counts as the top-level project's. A project path with a line break is refused, since the root is written on a comment line in the hook. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>