Merge supports folder hierarchy comparison and synchronization, enabling you to compare and merge entire directory trees. This is ideal for detecting changes in different versions of source code or web pages. You can even use the efficient byte-by-byte comparison option to verify the contents of recordable CDs or USB thumbsticks.
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. It might also be helpful to review the The Ribbon and the Toolbar: Making the Most of the Merge User Interface on Different Versions of Windows topic.
Starting a comparison
Use the New folder comparison 
button in the quick access toolbar (above the ribbon), the ribbon itself (or the drop-down menu for the leftmost ribbon item),
or the toolbar in the old-style Merge interface. Alternatively, press Ctrl+D.
The layout of the folder comparison window is very similar to that of the file comparison window.
Specifying the folders to compare
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.
To perform the comparison once you have chosen the two files to compare, click the Start or recompare 
button in the ribbon or toolbar, or press the Enter key while one of the folder name entry fields has focus.
You do not need to wait for the folder comparison to complete before viewing or using the results of the comparison.
As well as folders on the local disk and network volumes, Merge is also able to directly access and compare folder hierarchies within Perforce and Subversion repositories. See Virtual File System (VFS) Plugins for more details.
Accessing other revisions of a folder with the Versions button
If there are other versions of the folder named in the entry field available for comparison, the 
button displays a list of these other versions. You can open the same file in both the left and right comparison panes, then
use this button to compare a file with an earlier revision of itself.
When the Options… > Application > Show file versions from SCM systems option is checked, Merge endeavours to find any other versions of the folder you are comparing from the relevant configuration management system repository. If a Perforce, Subversion, Visual SourceSafe, Mercurial, or Git URI has been specified in the filename entry field, Merge will search the repository from which it accessed the folder for any other revisions. Otherwise, if a folder has been loaded from the local disk or a network volume and is part of a client workspace, Merge will search the relevant repository for which credentials have been supplied on the Credentials options page.
If the Options... > Application > Show file and folder versions from System Restore option is checked, Merge will show any versions of the folder you are comparing that have been stored by Windows System Protection or the Araxis Snapshot Service. For more information, see Accessing Versions Stored by Windows System Protection or the Araxis Snapshot Service.
If the button is not enabled, check the relevant options on the Application and Credentials options pages.
Three-way folder comparisons
In addition to two-way folder comparisons, the Professional Edition of Merge supports comparisons between three folder hierarchies and automatic folder merging.
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 ribbon or toolbar Options 
menu Show timestamps and sizes command to turn 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 Show changes column command in the ribbon or toolbar Options 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 commands in the ribbon or toolbar Select rows
menu to select rows in a variety of different ways.
-
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.
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Press Ctrl+A to select all the files in the results list.
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 
ribbon or toolbar command.
You can usually 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 command in the ribbon or toolbar Hide/reveal 
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 files, you might want to set bookmarks to enable you to return to locations of interest later
on. Press Ctrl+F2, or click Edit comment 
in the ribbon or toolbar, to toggle a bookmark on or off on the current line. To navigate between bookmarks, press F2 or Shift+F2, or use the Next bookmark 
and Previous bookmark 
buttons in the ribbon or toolbar.
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 create an HTML comparison report or 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.
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.