Smart Merge

Create a unity plugin that allows you to launch the scene merging tool, Unity Smart Merge, from unity. It could be a right click interface or an inspector interface.

• Right click - when you have 2 sceens selected at the same time and the user right clicks add an option to launch to tool
• Inspector - The user can drag the scenes into fields and click a button that launches the tool 

Unity Scene Merge documentation

Command line interface example:

'C:\Program Files\Unity 5.6\Editor\Data\Tools\UnityYAMLMerge.exe' merge -p "$BASE" "$REMOTE" "$LOCAL" "$MERGED"