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README Edits and Expanded How to Run Section (kgrzybek#20)
* Table of Contents initial fixes * Filled out How to Run section. * Editing done through 2.1. * Couple small tweaks - still through 2.1 only. * Edits through 3.2 * Edits through 3.3. * Edits through 3.4. * Edits through end of doc. Only final check to conduct. * Final edits. * Final final edits.
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