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The Diff dialog window lets you select the files or folders you want to compare and lets you specify many options. There are four buttons in this window:
Two buttons with a left or a right bended arrow icon let you apply the currently selected difference from one frame to the other. Once a diff has been applied, the buttons are dimmed. If you click on one of these buttons while pressing the option key, then all diffs will be applied simultaneously.
Two small round buttons, located just over the frames, let you save the changes in the corresponding files. If one of the files has been modified, the button indicates it with a black spot.
Collating does not apply to folders.
On the top of the window, two popup menus let you specify if you want to compare two files or two folders and select the output format. This output format is not relevant when you are collating files. The Brief format will only tell whether the files are different or not, without displaying the differences. With the side-by-side format, it is recommended to turn the "expand-tab" option on.
All the options correspond to a switch of the command line GNU Diff tool. They have the same name and are explained in this documentation. The only exception concerns the Eol1 and Eol2 popups in the "Advanced options" panel: Diff'nPatch is able to compare files with different line endings: Macintosh files have 'cr' line endings, Unix files have 'lf' line endings and Windows files have 'crlf' line endings. By default Diff'nPatch will try to guess which is the type of the files you want to compare (the 'Intuit' item), but you can also specify it explicitly. 'Eol' stands for "end of line".