updated makefile and .gitignore to us latexmk instead of rubber

paper_template/Makefile

@@ -1,7 +1,11 @@
 #!/usr/bin/make
 
 all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
-pdf: all
+
+# use the following section for Rnw/knitr documents
+# all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
+# %.tex: %.Rnw
+#	Rscript -e "library(knitr); knit('$<')"
 
 refs-processed.bib: 
 	perl -p -e 's/©//' refs.bib > refs-processed.bib
@@ -9,21 +13,23 @@ refs-processed.bib:
 	recode -d u8..ltex < refs-processed.bib | sponge refs-processed.bib
 
 %.pdf: %.tex refs-processed.bib
-	rubber -fd $<
+	latexmk -f -pdf $<
 
 clean: 
-	rubber -d --clean *.tex
+	latexmk -C *.tex
 	rm -f *.tmp
 	rm -f vc
 	rm -f refs-processed.bib
+	# the following lines are useful for Rnw/knitr
+	# rm -rf cache/ figure/
+	# rm -f *.tex
 
 viewpdf: all
 	evince *.pdf
 
-spell:
-	aspell -c -t --tex-check-comments -b text.tex
-
 vc:
 	vc-git
 
+pdf: all
+
 .PHONY: clean all