Function compile_program_with_modules 

pub fn compile_program_with_modules(
    items: &[TopLevel],
    arena: &mut Arena,
    module_root: Option<&str>,
    source_file: &str,
    analysis: Option<&AnalysisResult>,
) -> Result<(CodeStore, Vec<NanValue>), CompileError>

Compile with explicit module root for depends resolution.