While the "preprocessor command" option is useful for processing single files, it is not very helpful when processing directories containing several different types of files. It's seldom appropriate to use the same preprocessor on every file. It would be helpful to be able to associate different file types (i.e. different file extensions) with different preprocessors (and if a file type is not specified, no preprocessor at all). This also has the advantage of not having to change preprocessor settings every time a different file type is compared when comparing single files.
Another approach would be to provide an option to pass the preprocessor the input file path on its command line, instead of piping the input file directly to it. The preprocessor could then decide for itself how to handle different file types. "weiehpcc" has suggested a similar approach, though his approach is probably more flexible.
Thanks,
Elle