I’m using UE 4.14 built from the GitHub sources and packaging my game for Windows 64-bit.
Packaging finishes without errors but some files end up in WindowsNoEditor/<MyGame>/Editor/Engine instead of WindowsNoEditor/Engine.
The game works when I move those files to the correct location but that’s obviously just a workaround, I’d like to know what’s causing this problem.
I haven’t tried packaging the game for a long time but it definitely worked correctly with UE 4.12.
I found what’s causing this problem in Source\Programs\AutomationTool\AutomationUtils\DeploymentContext.cs.
The way paths are determined to be project relative or engine relative is by checking if they start with either ProjectRoot or LocalRoot.
In my case ProjectRoot is H:<MyGame> and LocalRoot is H:<MyGame>Editor.
Both start with H:<MyGame> therefore the engine files are assumed to be project files and end up in the wrong directory.
Renaming the editor’s directory so it doesn’t start with the project name is a workaround for now but this definitely should get fixed.