First, you need to identify which artifact is not being handled correctly anymore. It’s explicit in the error message: if it says Error: It seems the App source…' the problem is app. The pattern is the same across all artifacts.
Fixing this error is typically easy, and requires only a bit of time on your part. Start by downloading the package for the cask: brew cask fetch {{cask_name}}. The last line of output will inform you of the location of the download. Navigate there and manually unpack it. As an example, lets say the structure inside the archive is as follows:
.
├─ Files/SomeApp.app
├─ Files/script.sh
└─ README.md
Now, let's look at the cask (brew cask cat {{cask_name}}:
(…)
app 'SomeApp.app'
(…)
The cask was expecting SomeApp.app to be in the top directory of the archive (see how it says simply SomeApp.app) but the developer changed it to inside a Files directory. All we have to do is update that line of the cask to follow the new structure: app 'Files/SomeApp.app'.
Note that occasionally the app’s name changes completely (from SomeApp.app to OtherApp.app, let's say). In these instances, the filename of the cask itself, as well as its token, must also change. Consult the token reference for complete instructions on the new name.
Follow the instructions to submit a fix, and make the change to the cask. If using cask-repair, you may give it the --edit-cask flag when calling it on the command-line to step right into editing it. If you’re having trouble, open an issue explaining your steps so far and why you’re having trouble submitting the update.