Added bibliography, changed makefile

Makefile

@@ -21,15 +21,48 @@ $(NOTES_PDFS): $(NOTES)
 thesis_pdf/:
 	mkdir $@
 
-$(THESIS_PDF): $(THESIS) thesis_pdf/
-	xelatex $<
-	xelatex $<
-	mv thesis.* thesis_pdf/
-	cp thesis_pdf/thesis.pdf .
+$(THESIS_PDF): $(THESIS) LaTeX/thesis.bib
+	mkdir temp
+	cp -r LaTeX/fig .
+	cp -r LaTeX/flowcharts .
+	cp -r LaTeX/thesis.tex .
+	cp -r LaTeX/macros.tex .
+	cp -r LaTeX/thesis.bib .
+	cp -r LaTeX/thesis.cls .
+	xelatex thesis
+	bibtex thesis
+	xelatex thesis
+	xelatex thesis
+	rm -rf fig
+	rm -rf flowcharts
+	cp thesis.pdf temp/.
+	rm -rf macros.tex
+	rm -rf thesis.*
+	cp temp/thesis.pdf .
+	rm -rf temp
 
-.PHONY: clean
+.PHONY: clean revise
 
 clean:
 	rm -rf $(THESIS_PDF)
 	rm -rf $(NOTES_PDFS)
 	rm -rf thesis_pdf
+
+revise: $(THESIS) LaTeX/thesis.bib
+	mkdir -p temp
+	cp -r LaTeX/fig .
+	cp -r LaTeX/flowcharts .
+	cp -r LaTeX/thesis.tex .
+	cp -r LaTeX/macros.tex .
+	cp -r LaTeX/thesis.bib .
+	cp -r LaTeX/thesis.cls .
+	xelatex thesis
+	bibtex thesis
+	xelatex thesis
+	xelatex thesis
+	rm -rf fig
+	rm -rf flowcharts
+	cp thesis.pdf temp/.
+	rm -rf macros.tex
+	rm -rf thesis.*
+	cp temp/thesis.pdf .