Bug fix for dolt_commit leaving a dirty working set

go/libraries/doltcore/sqle/dsess/transactions.go

@@ -191,6 +191,10 @@ func doltCommit(ctx *sql.Context,
 			if err != nil {
 				return nil, nil, err
 			}
+			
+			// We also need to update the working set to reflect the new staged root value
+			workingSet = workingSet.WithStagedRoot(pending.Roots.Staged)
+			
 			logrus.Tracef("staged and HEAD merge took %s", time.Since(start))
 		}
 	}