Hi Jamie, thanks for the answer.
I just tried again with 4.2.1, but the result is the same. I am doing the same as b14de and just add the absolute paths to “Directories to always cook”. I have added paths to my ‘Blueprints’ folder and to a specific folder under ‘Blueprints’ where I know an asset is ignored.
For testing I disabled ‘Use Pak file’, so I can directly see which assets are cooked. The unreferenced asset is not in the cooked content folder, another asset in the same folder (that is directly referenced) is there.
I am not building from source right now, so I cannot easily test the change to CookCommandlet.cpp you mentioned in your answer to b14de.
I also tried manually calling RunUAT.bat again and it still works. The unreferenced assets are correctly placed in the output folders. The exact line is:
"C:\Program Files\Unreal Engine\4.2\Engine\Build\BatchFiles\RunUAT.bat" BuildCookRun -project=<PATH_TO_PROJECT_FILE>.uproject -CookDir="<PATH_TO_BLUEPRINT_FOLDER>" -noP4 -platform=Win64 -clientconfig=Development -serverconfig=Development -cook -maps=AllMaps -NoCompile -stage -archive -archivedirectory="Output Directory"