Now I am copying the remote files to a new sub-directory and then running WinMerge manually.
It would make my world a lot more pleasant if I could just pick 1 or more files and send them to WinMerge. Maybe copy the remote files into a temporary local folder 1st then run WinMerge on them. I think many others could benefit from this also.
Looking forward to some wonderful ideas. I am willing to experiment and post my results but I need some direction on the proper way I should go about this.