.rej files are rejected files (usually hacks, but not only).
When you receive these files after merging, you will have to manually edit them, fix them, and then apply them back.
You can read more about it here and what it is.
.rej file
diff a.txt (rejected hunks) ....
Fix it manually, and then apply the .rej files as a regular patch.
manually merge the change from *.rej to the required file and delete the *.rej file.
Another useful article on this subject can be found here .
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