It would be nice if I could tell SynchronizeIt/CompareIt to not compare files that have a special character string in the first line of the file.
For example, I have 2 projects where most files are identical, but not all. In those files that are unique to a single project, I put a comment in the first line to indicate that. If SI/CI could automatically check for this, that would be awesome! Then it would only compare the files that are supposed to match, and not those that I know to be different.
BTW, these are great tools that I enjoy using!