Function fill_transcripts 

pub fn fill_transcripts(
    iteration_dir: &Path,
    harness: Harness,
    mechanism: DispatchMechanism,
    subagents_dir: Option<&Path>,
    overwrite: bool,
) -> Result<FillTranscriptsResult, PipelineError>

Populate tool_invocations for every run.json under iteration_dir. See the module docs for the transcript sources and overwrite semantics.