Update thesis content and improve reproducibility framework

- Refine introduction and background chapters for clarity and coherence.
- Enhance reproducibility chapter by connecting challenges to infrastructure requirements.
- Add new references to support the thesis arguments.
- Update .gitignore to include IDE files.
- Modify hyperref package usage to hide colored boxes in the document.

thesis/thesis.tex

@@ -4,7 +4,7 @@
 %\usepackage{graphics}            %Select graphics package
 \usepackage{graphicx}             %
 %\usepackage{amsthm}              %Add other packages as necessary
-\usepackage{hyperref}             %Enable hyperlinks and \autoref
+\usepackage[hidelinks]{hyperref}  %Enable hyperlinks and \autoref, hide colored boxes
 \begin{document}
 \butitle{A Web-Based Wizard-of-Oz Platform for Collaborative and Reproducible Human-Robot Interaction Research}
 \author{Sean O'Connor}