To reach this options page, select View > Options... > Folder Comparisons > Launch Behaviour
The controls on this page are used to control how the folder comparison window opens file comparisons.
Minimize the window after opening file comparison views
When this option is checked, folder comparison windows will automatically minimize themselves after opening file comparison windows. If the number of open file comparison windows is being limited then the window will not minimize itself until it has been able to open all the file comparison windows.
Automatically close if files were identical
Check this option to automatically close newly opened comparison windows if there are no differences between the compared files. This option can be useful if you have deselected the Always check file content option in the Folder Comparisons options page.
Open a maximum of # comparisons at a time
Limits the number of views that the folder comparison facility will open at any one time.
Once you’ve examined and closed some of the opened comparison windows that were opened, you can click the 
button again and some more file comparison windows (up to the limit) will be opened. If you have the Minimize the window after opening file comparison views option checked, the folder comparison window will minimize itself when there are no more files to compare.
A double click on a folder row expands/collapses the row
Check this option to make folder rows expand/collapse when double clicked.
... opens a new folder comparison window for that row
Check this option if you would like Merge to open a new folder comparison window showing just the files and folders contained within the double clicked folder.
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