The scratch area is a special area in your applications executable file where you can store and later retrieve data.
The data you write to the scratch area is automatically encrypted for you on each write and decrypted when you read it back. The scratch area will grow and shrink automatically to accomodate the amount of data you store.
Because writing to the scratch area modifies your executable file this feature is incompatible with applications that attempt to wrap your executable like third party security applications, or that modify it or append data to it like code signing applications.
The Scratch commands are not available (they will return an error) if you select the Unbundled executable type on the Output Tab.