Function analyze_with_parse_result 

pub fn analyze_with_parse_result(
    config: &ResolvedConfig,
    modules: &[ModuleInfo],
) -> Result<AnalysisOutput, FallowError>

Run the analysis pipeline using pre-parsed modules, skipping the parsing stage.

This avoids re-parsing files when the caller already has a ParseResult (e.g., from fallow_core::extract::parse_all_files). Discovery, plugins, scripts, entry points, import resolution, graph construction, and dead code detection still run normally. The graph is always retained (needed for file scores).