Function analyze_retaining_modules 

pub fn analyze_retaining_modules(
    config: &ResolvedConfig,
    need_complexity: bool,
    retain_graph: bool,
) -> Result<AnalysisOutput, FallowError>

Run the full analysis pipeline, retaining parsed modules and discovered files.

Used by the combined command to share a single parse across dead-code and health. When need_complexity is true, the ComplexityVisitor runs during parsing so the returned modules contain per-function complexity data.

Errors

Returns an error if file discovery, parsing, or analysis fails.