Add missing transaction version update to Migration

Also, refactor the code so the entity changes are transaction-based and propagated to the entity on transaction commit, instead of being applied in-place. This should make the migration logic as well as the values observed when debugging clearer.

server/src/main/java/io/spine/server/entity/Migration.java

@@ -195,6 +195,7 @@ final void finishCurrentOperation() {
  Transaction<I, E, S, ?> tx = startTransaction(entity);
  EntityLifecycleMonitor<I> monitor = configureLifecycleMonitor(id);
  tx.setListener(monitor);
+ currentOperation().tx = tx;
  return tx;
  }
 
@@ -238,6 +239,7 @@ private static class Operation<I,
  private boolean physicallyRemoveRecord;
 
  private final E entity;
+ private @MonotonicNonNull Transaction<I, E, S, ?> tx;
  private final RecordBasedRepository<I, E, S> repository;
 
  private @MonotonicNonNull Event systemEvent;
@@ -249,16 +251,18 @@ private Operation(E entity, RecordBasedRepository<I, E, S> repository) {
 
  private void updateState(S newState) {
  if (!entity.state().equals(newState)) {
- entity.updateState(newState, increment(entity.version()));
+ tx.builder().mergeFrom(newState);
+ Version version = increment(entity.version());
+ tx.setVersion(version);
  }
  }
 
  private void updateLifecycle() {
  if (archive) {
- entity.setArchived(true);
+ tx.setArchived(true);
  }
  if (delete) {
- entity.setDeleted(true);
+ tx.setDeleted(true);
  }
  }