The "lib/applibs" directory is not created automatically when an instance is created, even though the directory exists in the DAS.
This is important for supporting config-specific libraries. The --libraries option of the deploy command accepts a relative pathname that is interpreted relative to the lib/applibs directory. When specifying a config-specific library using ../../config/named-config/lib/somesuch.jar, the reference fails if the lib/applibs directory does not exist.
The fix for this issue should cause the lib/applibs directory to show up in an instance even if there are no files in it.