Moved user packages and references to subdirectories

Makefile

@@ -1,40 +1,44 @@
 OUT_DIR := out
-$(shell mkdir -p $(OUT_DIR))
 GRAPHS_DIR := graphs
 CONTENTS_DIR := contents
+REFERENCES_DIR := references
 
 CONTENTS := $(wildcard $(CONTENTS)/*.tex)
+REFERENCES := $(wildcard $(REFERENCES_DIR)/*.bib)
 GRAPHS := $(wildcard $(GRAPHS_DIR)/*.gv)
 GRAPHS_IMG := $(GRAPHS:$(GRAPHS_DIR)/%.gv=$(OUT_DIR)/%.gv.png)
 
-.PHONY: all preview clean references pdf
-
+.PHONY: all
 all: pdf
 
-$(OUT_DIR)/%.gv.png: $(GRAPHS_DIR)/%.gv
-	dot -Tpng $< -o $@
+$(OUT_DIR):
+	@mkdir -v $@
 
+$(OUT_DIR)/%.gv.png: $(GRAPHS_DIR)/%.gv | $(OUT_DIR)
+	dot -T png $< -o $@
+
+.PHONY: graphs
+graphs: $(GRAPHS_IMG)
+
+.PHONY: index
 index: $(OUT_DIR)/main.idx
 	makeindex $^
 
-
-references: annexes.bib references.bib
+.PHONY: references
+references: $(REFERENCES)
 	bibtex $(OUT_DIR)/annexes
 	bibtex $(OUT_DIR)/references
 
-#pdf: $(OUT_DIR)/main.pdf
-#$(OUT_DIR)/main.pdf: main.tex $(GRAPHS_IMG) $(CONTENTS)
-pdf: main.tex $(GRAPHS_IMG) $(CONTENTS)
-	pdflatex -output-directory $(OUT_DIR) $^
+--inner_pdf:
+	pdflatex -output-directory $(OUT_DIR) main.tex
 
-preview: $(OUT_DIR)/main.pdf
-	zathura $^
+.PHONY: pdf
+pdf: $(GRAPHS_IMG) --inner_pdf references index --inner_pdf
 
-document:
-	make
-	make index
-	make references
-	make
+.PHONY: preview
+preview: pdf
+	@zathura $(OUT_DIR)/main.pdf
 
+.PHONY: clean
 clean:
-	rm $(OUT_DIR)/*
+	@rm -frv $(OUT_DIR)