Fix AutoCommit handling of an ongoing halt checkpoint

core/vdbe/mod.rs

@@ -1275,6 +1275,10 @@ impl Program {
                     rollback,
                 } => {
                     let conn = self.connection.upgrade().unwrap();
+                    if matches!(state.halt_state, Some(HaltState::Checkpointing)) {
+                        return self.halt(pager, state, mv_store);
+                    }
+
                     if *auto_commit != *conn.auto_commit.borrow() {
                         if *rollback {
                             todo!("Rollback is not implemented");

testing/all.test

@@ -25,5 +25,4 @@ source $testdir/changes.test
 source $testdir/total-changes.test
 source $testdir/offset.test
 source $testdir/scalar-functions-printf.test
-# Disabled until https://github.com/tursodatabase/limbo/issues/1004 is fixed
-# source $testdir/transactions.test
+source $testdir/transactions.test