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Fix the Tree Reader JSON processing method.
The expected JSON string provided by tests was incorrect, and did not match the actual output of the Tree Command.
The JSON string is wrapped in square brackets (an array) at the top level.
This change fixes both the tests and the JSON object processing method.
It also increases the timeout on the Tree Command from 3 to 5 seconds, just in case someone wants to run Treescriptify on a large directory.