Best way to configure Linux kernel for a machine

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I normally do the kernel configuration on my machine like this - 

* copy the distro configuration file  to the kernel dir 
* make menuconfig (answer Y's/N's/M's) Normally keep return key pressed
for default answers
* then do the actual kernel compilation


Now, I know that this is not a clean way to do the kernel compilation
(although it has worked for me for thousands of times that I have
compiled and successfully booted up with the kernel - without any issues
- whatsoever !)

But this time , I am bent upon coming up with a configuration
specifically targeted to my machine. What is the best way to do this ?


Also, while creating a initrd image 

# mkinitrd /boot/initramfs.img 3.8.0-rc3+ -f 
ERROR: modinfo: could not find module ipt_MASQUERADE
ERROR: modinfo: could not find module iptable_nat
ERROR: modinfo: could not find module nf_nat
ERROR: modinfo: could not find module snd_hda_codec_intelhdmi
ERROR: modinfo: could not find module joydev

I got the above errors - I know how to resolve these errors , but want
to understand why in the first place mkinitrd should complain in the
first place ??

Thanks list for help for all these years.

-- Shraddha



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