Merging local changes with qq

Makefile, .gitignore and renamed files

Added a .gitignore file that should make commits easier

Makefile which uses latexmk to build a pdf for you via pdflatex. Has targets `view`, `clean` and `all`.

Rename of files to be consistent with the other files

See merge request !1

Reference list should only contain references used in the text, and should use numerical keys by default. Gave an example in the theory chapter