The System Integrity Protection (SIP) feature in macOS 10.11+ (El Capitan, Sierra, ...) prohibits system modifications and a "dirty hack" is needed to run this software-application "XtraFinder", as described on the website of XtraFinder. Read here also.
Split the Finder window into two windows to achieve better file handling; you can easily compare folders content and copy/move files between the 2 folders.
The System Integrity Protection (SIP) feature introduced in El Capitan prohibits system modifications that TotalFinder requires to run. While it is possible to run TotalFinder on the latest macOS, doing so requires disabling SIP and thus altering the default macOS security configuration.