Function run_with_options 

pub fn run_with_options(
    input: &Path,
    verbose: bool,
    include_tests: bool,
    save_to: Option<&Path>,
    max_loc_per_file: Option<usize>,
    include_docs: bool,
) -> Result<Arc<DirGraph>, String>

Public build() entry point matching the Python API — returns just the graph. Thin wrapper over run_with_options_stats; the stats it drops are the CALLS-resolution counters consumed by the code_tree_stats dev bin and the re-resolution phases. Single implementation, two entry points.