I want to merge each file in a directory (i.e. for different branches of the same code). I should be able to choose the files that I want to merge with filters (i.e. only source files, not images, etc).
Michael, this is the kind of thing that your version control tool should let you do, don't you think so?
Why don't you take a look at Plastic SCM (our version control! :-P), I think you'll find your answers there...