Restructured the project into folders to make things cleaner and easier to deal with.
Replaced a lot of \ref commands with \autoref commands to avoid inconsistent referencing of tables, chapters, appendices, etc, as well as to include the qualifier (Table, Chapter, Section, etc) in the hyperlink text.
Added /frontmatter, /mainmatter, and /appendix commands to main.tex to make page and chapter numbering more standard.