Ok well I auto-answer.
In fact the most important page on alterawiki (read it all carefully) is wiki/Linux_for_the_Nios_II_Processor.
The trick is in this part :
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Kernel development is currently taking place in the "unstable-nios2mmu" branch. It is stable despite the name. So to build a current (2.6.38 as of this writing), you need to switch to that branch for the kernel. Inside the "linux-2.6" folder, issue a "git checkout unstable-nios2mmu" command to switch your head to that branch.
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So to have device-tree support you need to switch the kernel to the branch unstable-nios2mmu
Hope it will help someone