diff

[Dave Martindale]

I use diff -D all the time.  When I use it to produce an output file
that will actually use cpp to generate one version or the other,
I always have to hand-edit it to get around the sort of problem that
you note.

However, I seldom use it for that.  My main use is producing a new
source file that contains the merged changes from two different
versions of basically the same code.  Wherever the two pieces of code
differ, the diff output allows me to see the differences in context,
side-by-side, and I selectively discard the lines of code that I don't
want, leaving the version that I do.