I wasn't about to scroll through both directories to find the culprit and tried both Kompare and Meld but they didn't do what I wanted. Off to StackOverflow where I found the comm command. This command will give you files that are in dir1 and not in dir2:
comm -23 <(ls dir1 |sort) <(ls dir2|sort)From man comm:
lines unique to FILE2, and column three contains lines common to both files.
-1 suppress column 1 (lines unique to FILE1)
-2 suppress column 2 (lines unique to FILE2)
-3 suppress column 3 (lines that appear in both files)
I also inadvertently copied stacks of files that I had renamed on one side but not the other so ended up with multiple copies. For this I discovered Fslint, a GUI duplicate finding program which did a fine job. It found hundreds of files which were the same but had different names. It matches md5 sums I believe.