Function generate_markdown 

pub fn generate_markdown(
    output_path: &str,
    input_dir: &str,
    filters: &[String],
    ignores: &[String],
    file_tree: &FileTree,
    files: &[DirEntry],
    base_path: &Path,
    line_numbers: bool,
    encoding_strategy: Option<&str>,
) -> Result<()>

Generates the final Markdown file.