In the java world it is common to have many source files moved among some directories. Diff-ing them misses out (as added or deleted) the ability to compare them from the directory compare.
Is there a setting (I didn't find it) to tell EdPro to sort on file name only?
I'm not exactly sure what you are asking but ExamDiff Pro can only meaningfully compare directory with matching file structures. If a file was moved from one subdirectory to another, EDPro will not match this file.