Function run_touch 

pub fn run_touch(
    db_dir: &Path,
    files: &[PathBuf],
    hook_stdin: Option<&str>,
) -> Result<StructureReport, CliError>

Re-extract exactly the files named, and nothing else.

files comes from argv when a caller has the paths; otherwise they are read out of a PostToolUse hook payload on stdin, the same way run_recall reads a prompt. Anything that is not a working-tree file this store already knows — a path outside the repository, an excluded one, one the graph has never seen — is dropped without comment, because a hook fires on every edit the assistant makes and most of them are none of this store’s business.