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When building the kernel26 package, does it use the flags specified in makepkg.conf?
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Everthing that uses makepkg uses the flag, I think....
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No. The kernel uses a set of optimisations known to work for the kernel on the specified architecture. It is not recommended to change these, but i believe they are in the Makefile in the top directory of the kernel-tree.
If you want to change the flags the kernel is compiled with, you can check out zen-sources. It includes a patch so you can change the flags for the compiler and linker in the make <X>config stage
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