Merge enables you to synchronize the content of two folder hierarchies. As well as Launching File Comparisons, you can copy files and folders between folder hierarchies and delete files and folders.
Copying files and folders
To copy files and folders from one folder hierarchy into the other, first select those files and folders.
Next, click the Copy Selected 
toolbar button and select Copy from First to Second Columns… or Copy from Second to First Columns… to copy the files from one hierarchy into the other. When you select the menu item, a window will appear to show you which files will be copied and to where they will be copied.
The Source column lists all the selected files and folders. The Destination column shows you where those files and folders will be copied. You can choose a different destination (not necessarily in the folder hierarchies being compared) by changing the content of the Destination path entry field at the top of the window. The content of the Destination column will be updated to reflect the new destination.
Note that the location of a file relative to the folder comparison location is preserved when it is copied from one hierarchy to the other. For example, in a folder comparison between C:\documents and D:\documents, a file report.doc in a folder reports in the first folder hierarchy would be copied into a folder called reports in the second folder hierarchy.
Deleting files and folders
To delete items in the folder comparison window, select the files and folders that you want to remove, right-click, and use the Delete Selected Items in Column item in the context menu. You can undo a deletion by restoring the deleted files and folders from the macOS Trash.
Alternatively, the Actions▸Delete Selected menu item deletes all two/three way selected items, not just those in the column.
Some files and folders (particularly those located on network volumes) cannot be sent to the Trash. Merge will let you know if this occurs and will provide you with an opportunity to delete the files and folders permanently.
Resolving changes between different versions of a file
The help topic Launching File Comparisons explains how to resolve changes between different versions of a file instead of simply copying the most recent instance into the other folder.
Operating on multiple files
You will probably need to perform copy operations on several different selections of files and folders to fully synchronize folders. Clicking the Select Rows 
toolbar button and selecting Select by State…, or selecting the Actions▸Select Rows▸Select by State… menu item, enables you to select files and folders based on criteria you specify. See Comparing Folders for other ways to select files.
A typical scenario
A typical folder synchronization scenario ensuring that two folder hierarchies contain identical up-to-date content could involve the following operations:
- Select all changed files that are newer in the first folder and copy them into the second folder.
- Select all changed files that are newer in the second folder and copy them into the first folder.
- Identify all files marked as being removed from the first folder, delete the ones that you no longer need and copy the rest into the second folder.
- Identify all files marked as being added to the second folder, delete the ones that you no longer need and copy the rest into the first folder.