Function run_with_audit 

pub fn run_with_audit<R: BufRead, W: Write, A: Write>(
    reader: R,
    writer: &mut W,
    audit: &mut A,
    window_secs: u64,
    stage: Stage,
) -> Result<ReplayWithAudit>

Replay a JSONL stream through the core pipeline, mirroring every per-stage record into audit (volatility-stripped, sorted-key canonical form) and returning the SHA-256 of that canonical stream.

The audit stream omits the trailing summary record so the hash itself can be embedded into the summary without self-reference.