looks like I am missing something.

I got to branch A which I want to 'merge' (preserving the differencies) 
with branch B. 
I run git read-tree -m HEAD <branch B>
I get a number of files updated and added in my working folder. Files that 
were absent in branch A are added, the differenceis are applied. But 
unfortunately the differencies between the files are still erasing the old 
lines. I mean if there were difference in branch A and branch B on the same 
line in some file - after this command lines of that file in branch A where 
I run the command are replaced with lines from branch B. And there is no 
conflict. So it loooks like typical merge.

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