Cleaned up and fixed Makefile

This closes #3. The export from LyX to LaTeX was improperly done
as plain latex instead of pdflatex, which is why the "EPS" files
were showing up. I also cleaned up the Makefile to make it a bit
more friendly, as well as automatically rerunning pdflatex so
that all references are updated properly.

.gitignore

@@ -14,6 +14,7 @@ master/
 *.idx
 *.lof
 *.log
+*.lol
 *.out
 *.toc
 *pk

Makefile

@@ -1,12 +1,20 @@
-all	: master
+all	: master.pdf
 
-master	: master.tex master.aux
+html	: master.tex master.aux
+	@echo [Building HTML]
 	latex2html -split 3 -local_icons master.tex
 
+pdf	: master.aux
+master.pdf	: master.aux
+
 master.tex	: master.lyx
-	lyx -e latex master.lyx
+	@echo [Exporting PDFLaTeX]
+	@lyx -e pdflatex master.lyx
 
 master.aux	: master.tex
-	pdflatex master.tex
+	@echo [Building PDF]
+	@bash -c "while pdflatex master.tex && grep -q \"Rerun to get cross-references right\" master.log ; do echo \"  Rebuilding references\" ; done"
+	@echo [Built PDF]
+
 clean:
 	rm -f *.tex images/*.eps *.toc *.aux *.dvi *.idx *.lof *.log *.out *.toc *.lol