Clean up on chapter 1

Minor clean up to chapter 1.
Minor edits to chap. 2

Minor cleanup and a simple spelling fix.
Moved info to Chp. 2, revision to chapter 3

Moved info from chapter 3 to chapter 2.  Cleaned up chapter 3.
Minor edit to chapter 4

Fixed label
minor edits to chapter 6

Minor edits to chapter 6.  Thesis has been checked for NEAT
calculations, relates to issue #23.  This finishes the sync to the
story board or issue #15.