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When I update to 10.2 will the sym link from /usr/src/linux be automatically modified from /usr/src/linux-2.4.28 to /usr/src/linux-2.4.31? If so, then how does that affect the currently installed 2.4.28 kernel I recompiled and installed?
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That link only affects the source, and will only be changed if you install another Kernel Source package. The link is really only a short-cut to the latest source you have loaded and isn't actually used when you compile a kernel, because you should already be inside that directory. As it's only a link to a directory, it won't affect your current kernel at all.
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What precautions do I need take to preserve my 2.4.28 recompiling before I begin trying to learn more about recompiling with the 2.4.31 kernel?
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Copy the .config file out of the kernel-2.4.28 directory. That way you can use it as a base for configuring under 2.4.31, using make oldconfig (I think). Unless you plan on compiling another kernel under 2.4.28, then you don't need to "force" the upgrade to leave your old source tree.
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If I recompile the 2.4.31 kernel and update the module dependencies, and my effort fails, will my previous 2.4.28 dependencies remain untouched and usable?
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If you only recompile, yes. But be careful upgrading the kernel-modules and kernel when you upgrade. You'll have to install those, not upgrade, or else it'll remove the old ones.
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I already maintain copies of my kernel, system.map and config file in my /boot partition and identified by a unique name such that any recompiling effort does not easily overwrite those files. I'm not sure how the kernel knows where to look for the modules, is that defined in the system.map or config file?
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The lilo, or grub (I'm assuming) configuration files tell it where the kernels reside, and what they're called. The modules are in /lib/modules/<kernel version>
Cheers,
Eddie