Program: 34692
Project: 34692
Buggy source:
public void generateInWorld(LargeStructureWorld world,Random rand){
  int xx, yy, zz, offX, offZ, fromX, fromZ, dir, dist;
  boolean prevStairs=false;
  List<int[]> stairs=new ArrayList<>();
  for (  LaboratoryElement room : roomElements) {
    if (room.type == LaboratoryElementType.SMALL_ROOM)     LaboratoryElementPlacer.generateSmallRoom(world,rand,room.x,room.y,room.z);
 else     LaboratoryElementPlacer.generateLargeRoom(world,rand,room.x,room.y,room.z);
  }
  for (  LaboratoryElement room : roomElements) {
    for (dir=0; dir < 4; dir++) {
      if (room.connected[dir]) {
        room.connected[dir]=false;
        offX=Direction.offsetX[dir];
        offZ=Direction.offsetZ[dir];
        fromX=xx=room.x + offX * (room.type.halfSizeX + 1);
        fromZ=zz=room.z + offZ * (room.type.halfSizeZ + 1);
        yy=room.y;
        dist=1;
        LaboratoryElementPlacer.generateRoomEntrance(world,rand,fromX - offX,yy,fromZ - offZ,offX != 0);
        CycleProtection.setCounter(512);
        while (CycleProtection.proceed()) {
          xx+=offX;
          zz+=offZ;
          ++dist;
          LaboratoryElement hall=getAt(xx,zz);
          if (hall == null) {
            LaboratoryElement nextRoom=null;
            for (int test=0, tx=xx, tz=zz; test < 16; test++) {
              LaboratoryElement element=getAt(tx+=offX,tz+=offZ);
              if (element != null) {
                nextRoom=element;
                break;
              }
            }
            if (nextRoom.y != yy) {
              xx-=offX;
              zz-=offZ;
              stairs.add(new int[]{xx,yy,zz,nextRoom.y - yy,dir});
            }
            LaboratoryElementPlacer.generateHall(world,rand,fromX,fromZ,xx - offX,zz - offZ,yy,offX != 0);
            if (nextRoom.y != yy) {
              xx+=offX;
              zz+=offZ;
              yy=nextRoom.y;
            }
            LaboratoryElementPlacer.generateRoomEntrance(world,rand,xx,yy,zz,offX != 0);
            break;
          }
 else           if (hall.y != yy) {
            LaboratoryElementPlacer.generateHall(world,rand,fromX,fromZ,xx - offX,zz - offZ,yy,offX != 0);
            stairs.add(new int[]{xx,yy,zz,hall.y - yy,dir});
            fromX=xx+=offX;
            fromZ=zz+=offZ;
            yy=hall.y;
            continue;
          }
          prevStairs=false;
        }
        CycleProtection.reset();
        dist+=room.type.halfSizeX * offX + room.type.halfSizeZ * offZ - 1;
        while (--dist >= 0) {
          LaboratoryElement ele=getAt(xx,zz);
          if (ele != null && ele.type.isRoom()) {
            ele.connected[Direction.rotateOpposite[dir]]=false;
            break;
          }
 else {
            xx+=offX;
            zz+=offZ;
          }
        }
      }
    }
  }
  for (  LaboratoryElement room : roomElements) {
    if (room.type == LaboratoryElementType.SMALL_ROOM)     LaboratoryContent.populateSmallRoom(world,rand,room.x,room.y,room.z);
 else     LaboratoryContent.populateLargeRoom(world,rand,room.x,room.y,room.z);
  }
  for (  int[] array : stairs)   LaboratoryElementPlacer.generateHallStairs(world,rand,array[0],array[1],array[2],Direction.offsetX[array[4]],array[3],Direction.offsetZ[array[4]]);
}

Fixed version (ground truth):
public void generateInWorld(LargeStructureWorld world,Random rand){
  int xx, yy, zz, offX, offZ, fromX, fromZ, dir, dist;
  boolean prevStairs=false;
  List<int[]> stairs=new ArrayList<>();
  for (  LaboratoryElement room : roomElements) {
    if (room.type == LaboratoryElementType.SMALL_ROOM)     LaboratoryElementPlacer.generateSmallRoom(world,rand,room.x,room.y,room.z);
 else     LaboratoryElementPlacer.generateLargeRoom(world,rand,room.x,room.y,room.z);
  }
  for (  LaboratoryElement room : roomElements) {
    for (dir=0; dir < 4; dir++) {
      if (room.connected[dir]) {
        room.connected[dir]=false;
        offX=Direction.offsetX[dir];
        offZ=Direction.offsetZ[dir];
        fromX=xx=room.x + offX * (room.type.halfSizeX + 1);
        fromZ=zz=room.z + offZ * (room.type.halfSizeZ + 1);
        yy=room.y;
        dist=1;
        LaboratoryElementPlacer.generateRoomEntrance(world,rand,fromX - offX,yy,fromZ - offZ,offX != 0);
        CycleProtection.setCounter(512);
        while (CycleProtection.proceed()) {
          xx+=offX;
          zz+=offZ;
          ++dist;
          LaboratoryElement hall=getAt(xx,zz);
          if (hall == null) {
            LaboratoryElement nextRoom=null;
            for (int test=0, tx=xx, tz=zz; test < 16; test++) {
              LaboratoryElement element=getAt(tx+=offX,tz+=offZ);
              if (element != null) {
                nextRoom=element;
                break;
              }
            }
            if (nextRoom == null) {
              Log.error("String_Node_Str");
              continue;
            }
            if (nextRoom.y != yy) {
              xx-=offX;
              zz-=offZ;
              stairs.add(new int[]{xx,yy,zz,nextRoom.y - yy,dir});
            }
            LaboratoryElementPlacer.generateHall(world,rand,fromX,fromZ,xx - offX,zz - offZ,yy,offX != 0);
            if (nextRoom.y != yy) {
              xx+=offX;
              zz+=offZ;
              yy=nextRoom.y;
            }
            LaboratoryElementPlacer.generateRoomEntrance(world,rand,xx,yy,zz,offX != 0);
            break;
          }
 else           if (hall.y != yy) {
            LaboratoryElementPlacer.generateHall(world,rand,fromX,fromZ,xx - offX,zz - offZ,yy,offX != 0);
            stairs.add(new int[]{xx,yy,zz,hall.y - yy,dir});
            fromX=xx+=offX;
            fromZ=zz+=offZ;
            yy=hall.y;
            continue;
          }
          prevStairs=false;
        }
        CycleProtection.reset();
        dist+=room.type.halfSizeX * offX + room.type.halfSizeZ * offZ - 1;
        while (--dist >= 0) {
          LaboratoryElement ele=getAt(xx,zz);
          if (ele != null && ele.type.isRoom()) {
            ele.connected[Direction.rotateOpposite[dir]]=false;
            break;
          }
 else {
            xx+=offX;
            zz+=offZ;
          }
        }
      }
    }
  }
  for (  LaboratoryElement room : roomElements) {
    if (room.type == LaboratoryElementType.SMALL_ROOM)     LaboratoryContent.populateSmallRoom(world,rand,room.x,room.y,room.z);
 else     LaboratoryContent.populateLargeRoom(world,rand,room.x,room.y,room.z);
  }
  for (  int[] array : stairs)   LaboratoryElementPlacer.generateHallStairs(world,rand,array[0],array[1],array[2],Direction.offsetX[array[4]],array[3],Direction.offsetZ[array[4]]);
}