Some makeup everywhere...

Makefile

@@ -1,13 +1,15 @@
 BASENAME=scientificcomputing-script
 
-SUBDIRS=programming statistics bootstrap likelihood pointprocesses 
-#spike_trains designpattern
-# regression
+SUBDIRS=designpattern statistics bootstrap regression likelihood pointprocesses 
+#programming  spike_trains
+SUBTEXS=$(foreach subd, $(SUBDIRS), $(subd)/lecture/$(subd).tex)
 
-pdf : $(BASENAME).pdf
+pdf : chapters $(BASENAME).pdf
+
+chapters :
 	for sd in $(SUBDIRS); do $(MAKE) -C $$sd/lecture pdf; done
 
-$(BASENAME).pdf : $(BASENAME).tex header.tex
+$(BASENAME).pdf : $(BASENAME).tex header.tex $(SUBTEXS)
 	export TEXMFOUTPUT=.; pdflatex -interaction=scrollmode $< | tee /dev/stderr | fgrep -q "Rerun to get cross-references right" && pdflatex -interaction=scrollmode $< || true
 
 clean :
@@ -17,5 +19,5 @@ clean :
 cleanall : clean
 	rm -f $(PDFFILE)
 
-watch :
+watchpdf :
 	while true; do ! make -q pdf && make pdf; sleep 0.5; done