4 files changed, 36 insertions, 41 deletions
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index c51f910..b57b3a9 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
 
 
 
@@ -329,12 +321,11 @@ $(project-package-contents): paper.pdf | $(texdir)
 	    paper.tex > $$dir/paper.tex
 
 #	Copy ONLY the version-controlled files in 'reproduce' and
-#	'tex/src'. This is important because files like 'LOCAL.conf' (in
-#	'reproduce/software/config') should not be archived, they contain
-#	information about the host computer and are irrelevant for
-#	others. Also some project authors may have temporary files here
-#	that are not under version control and thus shouldn't be archived
-#	(although this is bad practice, but that is up to the user).
+#	'tex/src'. This is important because the git commit hash goes in
+#	the tarball name (should correspond to it) and some project authors
+#	may have temporary files here that are not under version control
+#	and thus shouldn't be archived (although this is bad practice, but
+#	that is up to the user).
 #
 #	To keep the sub-directory structure, we are packaging the files
 #	with Tar, piping it, and unpacking it in the archive directory. So
@@ -362,17 +353,20 @@ $(project-package-contents): paper.pdf | $(texdir)
 	rm -rf $$dir/tex/build/build*
 
 #	If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
-#	PGFPlots was used to generate them), copy them too.
+#	PGFPlots was used to generate them), copy them too. Note that in
+#	the main project source, 'tex/tikz' is just a symbolic link to
+#	'tex/build/tikz'. But inside the tarball we do not want to have
+#	symbolic links and they should be independent.
 	if ls tex/tikz/*.pdf &> /dev/null; then
 	  cp tex/tikz/*.pdf $$dir/tex/tikz
 	fi
 
 #	When submitting to places like arXiv, they will just run LaTeX once
-#	and won't run 'biber'. So we need to also keep the '.bbl' file into
-#	the distributing tarball. However, BibLaTeX is particularly
-#	sensitive to versioning (a '.bbl' file has to be read by the same
-#	BibLaTeX version that created it). This is hard to do with
-#	non-up-to-date places like arXiv. Therefore, we thus just copy the
+#	and won't run 'biber' or 'biblatex'. So we need to also keep the
+#	'.bbl' file into the distributing tarball. However, BibLaTeX is
+#	particularly sensitive to versioning (a '.bbl' file has to be read
+#	by the same BibLaTeX version that created it). This is hard to do
+#	with non-up-to-date places like arXiv. Therefore, we just copy the
 #	whole of BibLaTeX's source (the version we are using) into the top
 #	tarball directory. In this way, arXiv's LaTeX engine will use the
 #	same BibLaTeX version to interpret the '.bbl' file. TIP: you can
@@ -521,7 +515,10 @@ $(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..a399637 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=$$(cat $(mtexdir)/project.tex)
@@ -166,9 +164,9 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies.tex \
 #	  for details.
 #
 #	  We need the modification to 'LD_LIBRARY_PATH' because we do not
-#	  build LaTeX from source and it uses '/bin/sh' (among other
-#	  possible system-wide things).
-	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
+#	  build LaTeX from source and it (or its packages) may use
+#	  '/bin/sh' (among other possible system-wide things).
+	  export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 	  biber paper
 	fi
@@ -200,9 +198,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 #	  option '-shell-escape'.
 #
 #	  We need the modification to 'LD_LIBRARY_PATH' because we do not
-#	  build LaTeX from source and it uses '/bin/sh' (among other
-#	  possible system-wide things).
-	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
+#	  build LaTeX from source and it (or its packages) may use
+#	  '/bin/sh' (among other possible system-wide things).
+	  export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 
 #	  Come back to the top project directory and copy the built PDF
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