Function refresh_all 

pub fn refresh_all(
    w: &mut Db,
    repo: &Path,
    prefix: &str,
    with_docs: bool,
) -> Result<StructureReport, CliError>

Refresh every working-tree file under prefix.

Writes in batches of [BATCH_FILES] files, one WAL commit per batch. Files whose stored props already match the working tree are left untouched.