The wrapper scripts allow you to use java cowsay as a command line tool.
Without them you must type this:
java -jar cowjay.jar "Hello"
The wrappers enable this:
cowsay "Hello"
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Create a directory on your computer to contain cowsay
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Add the cowsay directory to your PATH
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Download the wrapper scripts and put them in your cowsay directory. You can safely download all four of them regardless of platform (windows, linux or mac).
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Download the executable cowsay jar as described on the main page and put it in the cowsay directory.
The wrappers themselves contain more instructions.
The CLI is exactly like the original cowsay - no point documenting it here, google it.
The scripts look for the cowsay jar with the most recent modified time. To update simply download a newer version of the jar and put it in the directory.