13 files changed, 35 insertions, 41 deletions
diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh
index bea88d5..16950b5 100755
--- a/reproduce/analysis/bash/download-multi-try.sh
+++ b/reproduce/analysis/bash/download-multi-try.sh
@@ -31,7 +31,7 @@
 # reason, you don't want to use a lock file, set the 'lockfile' name to
 # 'nolock'.
 #
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf
index 5860806..7373503 100644
--- a/reproduce/analysis/config/INPUTS.conf
+++ b/reproduce/analysis/config/INPUTS.conf
@@ -105,7 +105,7 @@
 # also called '%' (if your local copy of the input dataset and the only
 # repository names are the same, be sure to set '%' accordingly).
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf
index ba8c960..80eb60a 100644
--- a/reproduce/analysis/config/delete-me-squared-num.conf
+++ b/reproduce/analysis/config/delete-me-squared-num.conf
@@ -1,6 +1,6 @@
 # Number of samples in the demonstration analysis (to be deleted).
 #
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index 1ab7de1..4c95c2f 100644
--- a/reproduce/analysis/config/metadata.conf
+++ b/reproduce/analysis/config/metadata.conf
@@ -15,7 +15,7 @@
 # and the copyright license name and standard link to the fully copyright
 # license.
 #
-# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf
index 7821306..e0400d3 100644
--- a/reproduce/analysis/config/pdf-build.conf
+++ b/reproduce/analysis/config/pdf-build.conf
@@ -12,7 +12,7 @@
 # LaTeX. Otherwise, a notice will just printed that, no PDF will be
 # created.
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf
index 031085d..09cca90 100644
--- a/reproduce/analysis/config/verify-outputs.conf
+++ b/reproduce/analysis/config/verify-outputs.conf
@@ -1,6 +1,6 @@
 # To enable verification of output datasets set this variable to 'yes'.
 #
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and
diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk
index a20abc6..1377395 100644
--- a/reproduce/analysis/make/delete-me.mk
+++ b/reproduce/analysis/make/delete-me.mk
@@ -1,6 +1,6 @@
 # Dummy Makefile to create a random dataset for plotting.
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 5150373..7aefd3f 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
 # Project initialization.
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -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
@@ -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
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index b1b794c..d2db4d3 100644
--- a/reproduce/analysis/make/paper.mk
+++ b/reproduce/analysis/make/paper.mk
@@ -1,6 +1,6 @@
 # Build the final PDF paper/report.
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -164,9 +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 "$$p"/paper.tex
 	  biber paper
 	fi
@@ -198,9 +198,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 #	  option '-shell-escape'.
 #
 #	  We need the modification to 'LD_LIBRARY_PATH' because we do not
-#	  build LaTeX from source and it uses '/bin/sh' (among other
-#	  possible system-wide things).
-	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$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/prepare.mk b/reproduce/analysis/make/prepare.mk
index ffb2a3c..352fd00 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
 # Basic preparations, called by './project make'.
 #
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index e87aed8..7286ca6 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -1,6 +1,6 @@
 # Top-level Makefile (first to be loaded).
 #
-# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index d2d1c14..8d1c2e0 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -4,7 +4,7 @@
 # are not included here. Please see that file for thorough comments on each
 # step.
 #
-# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index c74f8ca..4fedefd 100644
--- a/reproduce/analysis/make/verify.mk
+++ b/reproduce/analysis/make/verify.mk
@@ -1,6 +1,6 @@
 # Verify the project outputs before building the paper.
 #
-# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by