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Of course, Diff Commander very flexible in use and you can configure it as you wish. Diff Commander uses a set of rules (named as Profile) to determine whether the files are equal or it is necessary to include them in the results list as well as to determine the synchronization direction. You can customize all these rules in Profile combobox that can be seen at image below. Diff Commander allows you to create a set of such profiles. In each profile you can specify the options of comparison and synchronization.
Each Profile can be selected as active profile and applied only to both currently selected items in path selector comboboxes. It means that you can compare and synchronize at once only two folders or two other items. For comparing of many number of couples of items it is necessary to use Sessions.
List of session settings is same as profile settings, but have the list of pairs of comparing pathes also.