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updated logging explanation... still needs to be cleaned up for readability
added skeleton explanations for extensions and piping
how to install python and add python to PATH on windows platform
added how-to for alternative shells
Updated 12 How Do I Use atom python run (markdown)
Forgot to add in positional parameters sub-section for the Commands section.
Finally added the Commands section. Displays how to use the Command Field in detail.
Updated and touched up for posterity.
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