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.
Added the outline of the Proposed Work

Added the outline of the proposed sections for optimization to chapter-2
Updated gi
Wrote Secondary Electron Proposal and Methods

Added the secondary electron proposal and methods.  A little bit
uncertain where I should place the MLLD discussion, if any where.  I
kinda of want to throw it in as an appendix.
RPM Neutronics Introduction and Methods

Added an introduction to the RPM simulation and to the methods.  I need
to do some MCNP calculations to show the need for optimization. The RPM
methods came from DNDO-Detector, which might need to be modified a
little more.
Updated Neutronic Performance

Added more on the GA optimization technique and on the MCNPX modeling
and how that was accomplished.
Starting the Light Transport Section

Working on the introduction to the light transport.  So far have the
PNNL 14283 report summerized, but want to do the introducing
undergraduates to GEANT4 and the paper on polymerics / just using the
lightoutput from PPO.
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.