4 files changed, 16 insertions, 23 deletions
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index c51f910..1f2158a 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -265,16 +265,8 @@ clean:
 #	executing 'build'.
 	rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf
 
-#	Delete all the built outputs except the dependency programs. We'll
-#	use Bash's extended options builtin ('shopt') to enable "extended
-#	glob" (for listing of files). It allows extended features like
-#	ignoring the listing of a file with '!()' that we are using
-#	afterwards.
-	shopt -s extglob
-	rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex)
-	rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir))
-	rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/*
-	rm -rf $(badir)/preparation-done.mk
+#	Delete the full 'badir' (containing all analysis outputs).
+	rm -rf $(badir)
 
 distclean: clean
 #	Without cleaning the Git hooks, we won't be able to easily commit
@@ -285,7 +277,7 @@ distclean: clean
 #	'rm' program. So for this recipe, we'll use the host system's 'rm',
 #	not our own.
 	$$sys_rm -rf $(BDIR)
-	$$sys_rm -f .local .build $(pconfdir)/LOCAL.conf
+	$$sys_rm -f .local .build
 
 
 
@@ -521,7 +513,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
 #	    Unrecognized format.
 	    *)
-	    echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;;
+	    printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! "
+	    printf "Please see the description of this variable in "
+	    printf "'$(bsdir)/config/LOCAL.conf' for the acceptable "
+	    printf "values."; exit 1;;
 	  esac
 	fi
 
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 3c06ce3..b1b794c 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -105,8 +105,6 @@ else
 texbdir:=$(texdir)/build-$(shell whoami)
 endif
 tikzdir:=$(texbdir)/tikz
-$(texbdir):; mkdir $@
-$(tikzdir): | $(texbdir); mkdir $@
 
 
 
@@ -120,8 +118,8 @@ $(tikzdir): | $(texbdir); mkdir $@
 # on). Therefore, we should copy those macros here in the LaTeX build
 # directory, so the TeX directory is completely independent from each
 # other.
-$(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex
-	cp $(bsdir)/tex/*.tex $(mtexdir)/
+$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex
+	cp $(bsdir)/config/*.tex $(mtexdir)/
 
 
 
@@ -140,7 +138,7 @@ $(mtexdir)/dependencies.tex: $(bsdir)/tex/dependencies.tex
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
 $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \
-                      | $(mtexdir)/project.tex $(tikzdir)
+                      | $(mtexdir)/project.tex
 
 #	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 2689e64..e87aed8 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -19,9 +19,9 @@
 
 
 
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf
 
 
 
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index ea40f39..d2d1c14 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -23,9 +23,9 @@
 
 
 
-# Load the local configuration (created after running
-# './project configure').
-include reproduce/software/config/LOCAL.conf
+# Load the local configuration (created after running './project
+# configure').
+include .build/software/config/LOCAL.conf