hand-merged knitr material

- branch is now knitrified
- added material to the gitignore for tex files

paper_template/Makefile

@@ -1,11 +1,11 @@
 #!/usr/bin/make
 
-all: $(patsubst %.tex,%.pdf,$(wildcard *.tex)) 
+all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw)) 
 
 # use the following section for Rnw/knitr documents
 # all: $(patsubst %.Rnw,%.pdf,$(wildcard *.Rnw))
-# %.tex: %.Rnw
-#	Rscript -e "library(knitr); knit('$<')"
+%.tex: %.Rnw
+	Rscript -e "library(knitr); knit('$<')"
 
 %.pdf: %.tex 
 	latexmk -f -pdf $<
@@ -16,8 +16,8 @@ clean:
 	rm -f vc
 	rm -f *.bbl
 	# the following lines are useful for Rnw/knitr
-	# rm -rf cache/ figure/
-	# rm -f *.tex
+	rm -rf cache/ figure/
+	rm -f *.tex
 
 viewpdf: all
 	evince *.pdf
@@ -27,4 +27,4 @@ vc:	resources/vc-git
 pdf: all
 
 .PHONY: clean all
-# .PRECIOUS: %.tex
+.PRECIOUS: %.tex