If you haven’t already, spending a few moments browsing the Instant Overview of Folder Comparison and Synchronization will help you quickly become familiar with Merge folder comparisons.
Starting a comparison
Use the New Folder Comparison 
command in the File menu to open a folder comparison window. New folder comparisons may also be opened by clicking the appropriate toolbar button
or by pressing Ctrl+D.
The layout of the folder comparison window is very similar to that of the file comparison window. Enter the paths to the folders
you want to compare into the entry fields at the top of the window or use the browsing 
and history 
buttons. If you hold down the Ctrl key when selecting a folder from the drop-down list, Merge will fill the folder name fields for the other folder panels
with their corresponding historical values. You can also drag and drop folders from Windows Explorer onto the entry fields
in the folder comparison window.
When you have chosen the two folders to compare, click the Start/Recompare 
button in the toolbar or press Enter to start the folder comparison.
You do not need to wait for the folder comparison to complete before viewing or using the results of the comparison.
The folder comparison display
The screenshot above shows the results of a typical comparison between two folders. Background colours are used to indicate
the inserted, removed, changed, or unchanged state of each file or folder in the results list. The icon of the newest file
in any given row is indicated by a red dot 
adornment.
The folder comparison results list has a context menu that contains the most commonly used commands in the folder comparison window. Right-click within the results list to display the menu. Some of the commands in the menu will change depending on whether you click in the left or right side of the list.
You can use the controls in the Fonts and Colours Options dialog to change the colours that are used for inserted, removed, changed and unchanged files and folders.
Use the Toggle Timestamps 
button in the toolbar to toggle the display of file timestamps and sizes on and off.
The numbers in the Changes column show you the number of changes that have been made between the files in the two adjacent columns. For three-way folder comparisons, the third Changes column indicates the number of changes between the first and third folder hierarchies. You can toggle this column on and off using the Changes Column command in the View menu. Other symbols can appear in the changes column to indicate errors encountered while processing the files in a row, or to indicate that a row is filtered out by option settings. In either case, hover the mouse pointer over the symbol for more information about what it represents.
You can adjust the widths of the columns in the results list by dragging the column heading dividers from side to side.
Selecting files and folders
You can select files and folders in the results list in the following ways:
-
Use the Select... command in the Edit menu to select files and folders based on criteria you specify
-
Click on an item to select it and deselect any other selected items
-
Hold down Ctrl and click on an item to add or remove it from the current selection
-
Hold down Shift and click on an item to extend the selection to that item
-
Press Ctrl+A to select all the files in the results list
-
Use the controls in the Select Files and Folders window to select files and folders
Launching file comparisons
The results list can be used to launch file comparison windows for selected rows of files. Please see the Launching File Comparisons topic for more information.
Deleting files and folders
To delete files in the folder comparison window, select the files and folders that you want to remove and press the Delete key. Alternatively, use the Delete Selected... command in the Edit menu. You can undo a deletion by restoring the deleted files and folders from the Windows Recycle Bin.
Hiding files and folders
You can hide files and folders in the results list by selecting them and then choosing the Hide/Reveal Selected Items command in the View menu. You can later show all hidden items using the Show Hidden Items command on the same menu. Note that hidden items are not excluded from subsequent folder comparison operations. They will still be compared, but will not appear in the results list until you use the Show Hidden Items command.
Excluding files and folders from a comparison
You can specify wildcard expressions to exclude files and folders from the folder comparison. Files and folders that are excluded in this way will not be compared and will not appear in the results list even when you choose the Show Hidden Items command. You can use this feature to exclude large binary files or entire folder hierarchies from the comparison.
Bookmarks and comments
As you are comparing or editing folders, you might want to set bookmarks to enable you to return to locations of interest later on. Press Ctrl+F2 to toggle a bookmark on or off on the current line. To navigate between bookmarks, press F2 or Shift+F2.
Comments can be added to bookmarks, making it easy to note important information or to record a question. To edit a bookmark’s comment, right-click the bookmark and choose the Edit Comment menu item. Bookmark comments are shown as tooltips when you hover the mouse pointer over a bookmark.
Bookmarks and comments are included when you save a comparison for archival or team collaboration. They are therefore a useful tool for asking questions or making notes in a comparison that will later be emailed to other
team members for review.
Three-way folder comparisons
The Professional Edition of Merge supports comparisons between three folder hierarchies.
Customizing folder comparisons
There are a variety of options that can be adjusted to change the way that Merge performs folder comparisons. These options are discussed in the The Options Dialog topic.