Sorry, but this still isn't making a lot of sense to me.
2 files:
#1
AAAAAAAA
BBBBB
DDDDDDDD
#2
AAAAAAAA
CCCCC
DDDDDDDD
Mostly the same, with minor differences. What should the end result be?
Merge them, and which wins? The B's or the C's?
There are many applications that can show you the difference, or can tell you that they are the same or different, but I am not aware of anything that can 'know' how to merge like that.