Lightning branch

Separate chapter (2?) for lightning parameterization. Merge model
technical description and validation into case study chapter.
Intro to intro
Intro sections

Section 1 ozone chemistry
1.1 VOC sources + figures
Intro sections

Section 1.1
Finished up VOC section
Added ANOx section

Other changes:
Also added \lnox and \anox macros
Updated title
Chapter 1

Finished up lightning secition and chapter 1
Cooper figure

Added Cooper et al 2007 FTO3 figure to intro-intro paragraphs.

Other changes:
- transparent figures
- inverted orders of degrees in front matter
Chapter 1 proofread

Various proofread changes

Also added PDF to gitignore
Chapter 2

Copied GMD typesetted code into Chapter 2. Still need to clean up
references and layout, especially appendix regarding cloud-top
reduction.
Chapter 2 lightning tag

Added lightning path to section, figure, and table references
Chapter 2 fig cap

Changed figure captions in chapter 2 to support ToC summary
Chapter 2 figures

Added figure files to repository
Changed figure references to use thesis.cls macros

Updated several bibliographic references
Merging chapter 2 into master