NEW HAVEN — The Emancipation Proclamation, the seminal American document that freed the slaves, had a sweeping side effect many people don’t realize.

It changed the face of war. Thanks to Abraham Lincoln’s great Proclamation, America developed a blueprint for the conduct of war that would reverberate from 19th-century Appomattox to 21st-century Afghanistan.

“It’s a part of emancipation,” says Yale University law and history professor John Fabian Witt, author of the new book, “Lincoln’s Code: The Laws of War in American History,” Free Press, $32....