Use safe checkpointing before snapshots

The intention of the code is to do a checkpoint before starting to
write out the snapshot. Executing a manual checkpoint will at worst
make Litestream lose the track of the WAL as it will in specific
circumtances flush out the single page in the WAL file out.

Using the public checkpoint function of the database to issue a
managed passive checkpoint will ensure the sequence table is
written after and the position of the WAL isn't lost.

Fixes benbjohnson#521

replica.go

@@ -477,16 +477,16 @@ 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