Connecting HPS GPIOs to top level pins

The Qsys defines all HPS GPIOs as bi-directional signals. I have to define the top level IO pins as bi-directional too. Otherwise, it won't allow me to connect them together. However, I got warning messages when compiling the code:

Warning (13009): TRI or OPNDRN buffers permanently enabled

and there are a bunch of warnings of 13010 indicating which HPS IO pin has problem.

Firs question: how to get rid of the warning messages?

I also got another problem here: the software cannot read the GPIO input signals at gpio_swporta_dr .

it can only read the inputs at gpio_ext_porta.

Is this because of the warning message? or reading gpio_ext_porta is the only option for input signals?

thanks for inputs!

Qs Xiang