Edits to mybib, citation additions

Made comments to my bib to help me track what I have and have not cited
as well as making sure I had a copy of the reference in my Evernote.
Added some additional citations based on a few that was missed.
Appendix 1 re-write

Minor re-write to Appendix 1, changed URL to point to GitHub repos.
Additions to appendix 2

Added more content to appendix 2, should wrap up this appendix section
for review.
minor addition to chapter 3

Minor addition to chapter 3
Chapter 4 work

Added more on experiment and also another image.  One last image is
needed and a little more writeup, otherwise issue #2 is complete