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By this, I mean, while flashing a firmware (update.zip) from ClockworkMod recovery, is boot.img also flashed or do I need to use fastboot separately?

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What does the developer say?

Seriously every single rom that I've ever seen contained detailed instructions and more often than not a faq of some sorts for this reason exactly.

Anyway, if the zip file contains a boot.img file than it's safe to assume that it will be flashed. The updater-script that handles the copying of files is generated automatically when the rom is compiled so unless someone removes it, the kernel will be flashed.

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I just checked the updater-script and it doesn’t seem to handle the kernel (no lines concerning boot.img or anything) – kinokijuf Jul 22 '12 at 18:17
Hence the question at the top of the answer: What does the developer say? Did you just look at it or used grep/etc? In current rom it's package_extract_file("boot.img", "tmp/boot.img");write_raw_image("/tmp/boot.img", "boot"). The first part extract it, the second writes it to the boot partition. – Richard Borcsik Jul 22 '12 at 18:32

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