how diff between hardlink trees works?

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Hi,

I am not able to understand how diff between two trees of which one is just contains hardlinks to another's files (cp -al )ing
works.I am asking this question here because I need to build a custom kernel for which I need to generate patch. So the
documentation suggests to create a hardlink copy of the kernel source tree using cp -al and then make changes to
one of the trees and run a diff.I am wondering that if files are hardlinks then changes to one copy will affect another in which case
diff should give no output.
Also, the patch I created looks a little odd as it contains complete modified files instead of just the differences.
Please help!

Thanks
Vaibhav Jain
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