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I've downloaded the latest stable Linux kernel source (3.9.4), I'm running Xubuntu 13.04. I'd like to try to build my own kernel, as I'm quite comfortable at my hardware.

As suggested, I did the following:

root@localhost:/usr/src/linux-3.9.4# make clean
root@localhost:/usr/src/linux-3.9.4# make mrproper
root@localhost:/usr/src/linux-3.9.4# touch .config
root@localhost:/usr/src/linux-3.9.4# make menuconfig

I'm using touch .config because, without it, it's using some configuration from /boot. Why?

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You /should/ use the default configuration from /boot, at least as a base for your customization. Otherwise, checking the dozens (hundreds?) of options in menuconfig will take a lot of time. And your question makes me wonder whether you even have enough knowledge to do that. –  ignis Jun 5 '13 at 8:50
    
@ignis well I know. I know i can use make defconfig o use any previous configuration as base. But my actual question is: why is using that from /boot as base? –  user34295 Jun 5 '13 at 14:42

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