Since all the methods I tried does not work with GPIO, I decide to change another kernel.
There are over 20 .bb file in the recipes/linux/ directory. When you build with bitbake linux-omap, the OE will find one file with the following line in it.
DEFAULT_PREFERENCE_beagleboard = "1"
The file with the line will be the default one to build. I am going to try the latest one. 2.6.31.
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