Compare Window

Use the two left-most tool bar buttons (or corresponding menu items) to navigate through all modified blocks. The third tool bar button toggles the "Ignore Whitespace for Line Comparison" option. If the right text area is editable, you can easily take changes over from the left side by the right-most tool bar buttons (or corresponding menu items). Additionally you can use the small buttons in the center area, where the links between the left and right blocks are shown.

Edit|Preferences

The "Inner Line Comparison" option determines, how inner-line changes should be detected. Select the option, which suites your file type. All other options should be self-explanatory.