UPDATE: newer Jib versions have the feature to allow specifying a copy destination directory when using <extraDirectories>. You no longer have to manually prepare the target directory structure beforehand.
Create an empty directory <project root>/src/main/jib/dev/bus/usb/003/005 in your source repo.
Details
Jib allows adding arbitrary extra files and directories using the <extraDirectories> (Maven / Gradle) configuration. Files and (sub-)directories under <extraDirectories> will be recursively copied into the root directory of the image. By default, <project root>/src/main/jib is one such "extra directory", so you can simply create an empty directory with the structure you like.
You can also tune the permissions of files and directories using <permissions> if you want.