Removed excess file permissions

I removed excess file permisions to try and clean it up
Introductory Project Material

Adding background of this project (intro from Master's Thesis) as well
as some basic mechancism froman intial version of the SecElecKinEnergy
paper
Enchancing Introductory Material

Organized introduction.  Cleaned up copied material from SecEleKinE
paper, as well as moving text.
Modifying Introduction Material

Added text on the three areas of optimiziation, and removed abstract
text from the chapter-1.tex as well as some of the GEANT4 simulation
method details from the SecElecKinE paper.
Modified FrontMatter

Added the beginnings of an abstract (maybe change to exectutive
summary?) while removing the signature page from the proposal.  I need
to think of how I want to present this (what exactly) I am going for.
Merge branch 'ChapterOne'

Merging ChapterOne back to the main branch.  This is so I can work on creating the compiliation.
Merge branch 'ChapterTwo'

Adding the ChapterTwo Material back to the main branch, in order to work on compilation.
Merge branch 'FrontMatter'

Merging into the main branch in order to work on compilation.
Compilation fails on missing_figure

Working on getting the compilation to work.  I am getting
missing_figures, which I don't know means that it is not being found or
that my latex is messed up.
Merged and now compiles

Main document DisserationProposal.tex updated to compile and work with
the Latex-base submodule.  In addition, I got the missing figure to
work, and corrected some compilation errors.
Updated Vita

Updated vita to include Masters degree, and changed a litle bit of the
wording.  The base content was copied from my Master's Thesis.
Merge branch 'BackMatter'

Added the BackMatter to the main development.
Fixed PNNL 14283 Citation

Fixed the PNNL 14283 citation
A very rough draft

Rough cut timber draft of the Proposal.  Now going to refine the
sections with edits.
Submodule Latex-Base commit

Updating the Latex-Base Submodule.  This may break everything ...
Updated .gitignore

Updated the git ignore file to not track the main PDF file