Merging Folder Contents
Kaleidoscope can help you merge the differences between folders you are comparing.
Note that Kaleidoscope does not automatically merge contents of folders. When you decide to copy a folder from A to B and a folder with the same name exists in B, the entire contents of that folder will be overwritten.
Choosing Items to Copy
Select an item then select Merge > Copy A to B (or Copy B to A)
Select an item then click the Copy A to B (or Copy B to A) button in the toolbar at the bottom of the window.
An arrow will appear in the center column to indicate the selected copy direction.
You can also interact with the arrows in the center column to assign copy direction or clear the selection.
Hover the mouse cursor in the center column next to a changed or unmatched item.
An arrow will appear indicating the copy direction options.
Click the arrow to set the copy action.
You can click the arrow again to toggle through the copy direction options or to clear the copy action.

Copy or Clone Folders
There are separate options for copying and cloning folders, each designed for different scenarios.
Copy
Copy preserves your destination folder’s existing content while bringing over only the changes you see. This is the default behavior.
When you copy a folder from A to B, all the items that you see in Kaleidoscope’s outline will be copied over, at any depth. Items that only exist in the destination but not the source side will remain untouched. And, if there are items not shown in the source (invisible or ignored items), those won’t be copied.
In fact, when you select a folder to be copied, a copy operation will be applied to all those visible items, but not to the folder itself, as the folder will not really be copied, only its contents. This approach has two implications:
The folder will show a greyed out arrow. This means that parts of that folder will be copied.
You can fine-tune the operation by deselecting specific items or even copying some items in the opposite direction. The arrows will update to show what will happen.
Clone
Clone completely replaces the destination folder—useful when you want an exact replica, but potentially destructive.
If you select a folder to be cloned, the following will apply: if a folder with the same name exists in the destination, it will first be deleted. Then the folder will be copied over in its entirety, with all its potentially hidden and ignored items. As a result, whatever was in the folder on the destination side has been deleted and will be gone forever.
This behavior makes sense in certain scenarios, but it’s far more dangerous and should be used with caution. Trigger clone in three ways:
Hold down the ⌥ (option) key while clicking in the gutter between side A and B. A filled and stroked arrow will indicate the clone mode.
Bring up the menu next to the A to B or B to A button in the bottom toolbar. There you will find a separate entry for cloning.
Hold down ⌥ (option) while looking at either the Merge menu or the context menu of an item in the folder outline.
The visual clues when cloning a folder are very different from copying:
The cloned folder has an arrow wich is filled and has a border.
Items to be copied within that folder will show a lighter solid arrow, indicating that those items will be copied, but cannot be modified.
You’ll see a trash icon for items on the destination side that will be deleted when cloning from the source.
Review & Copy
Click the Copy… button in the lower right of the window to review your changes and start the copy operation. Alternatively, select Merge > Start Copying Files from the menu.
Unlike the regular comparison outline, the Confirmation View groups changes by operation, showing you a clear picture of what will happen when you start copying.

Deleting Files
Kaleidoscope does not support deleting files from the folder comparison. As explained above, a clone operation can result in implicit deletions. To directly delete an item:
Control-click (or right-click) the item and choose Reveal in Finder.
A Finder window will open with the item selected which you can then delete.