Use safe checkpointing before snapshots (#522)

replica.go

@@ -482,16 +482,16 @@ func (r *Replica) Snapshot(ctx context.Context) (info SnapshotInfo, err error) {
 	r.muf.Lock()
 	defer r.muf.Unlock()
 
-	// Prevent checkpoints during snapshot.
-	r.db.BeginSnapshot()
-	defer r.db.EndSnapshot()
-
 	// Issue a passive checkpoint to flush any pages to disk before snapshotting.
-	if _, err := r.db.db.ExecContext(ctx, `PRAGMA wal_checkpoint(PASSIVE);`); err != nil {
+	if err := r.db.Checkpoint(ctx, CheckpointModePassive); err != nil {
 		return info, fmt.Errorf("pre-snapshot checkpoint: %w", err)
 	}
 
-	// Acquire a read lock on the database during snapshot to prevent checkpoints.
+	// Prevent internal checkpoints during snapshot.
+	r.db.BeginSnapshot()
+	defer r.db.EndSnapshot()
+
+	// Acquire a read lock on the database during snapshot to prevent external checkpoints.
 	tx, err := r.db.db.Begin()
 	if err != nil {
 		return info, err