Function reconcile_changes 

pub fn reconcile_changes(
    store: &mut Store,
    repo_id: &str,
    source: &mut dyn SyncSource,
    paths: &[String],
    ts: &str,
    git_head: Option<&str>,
    config: &Config,
) -> Result<CheckpointResult>

Fetch every path through the source (None → gone), observe_batch, record the checkpoint exactly as §4.1.