Imported recent updates in Maneage, conflicts fixed

Until now, Maneage had undergone some updates.

With this commit, those updates have been imported and the conflicts that
resulted were fixed. They were all cosmetic and had no effect on the
analysis. The most significant one was about the change in the format of
'INPUTS.conf'.

In the process, I also noticed that the IEEEtran LaTeX package is now
called 'ieeetran' (the 'tlmgr' of TeXLive 2022 was failing).

14 files changed, 404 insertions, 367 deletions

diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try
index 76eb859..994a8fa 100755
--- a/reproduce/analysis/bash/download-multi-try
+++ b/reproduce/analysis/bash/download-multi-try
@@ -6,7 +6,7 @@
 #
 #   $ /path/to/download-multi-try downloader lockfile input-url downloaded-name
 #
-# NOTE: The `downloader' must contain the option to specify the output name
+# NOTE: The 'downloader' must contain the option to specify the output name
 # in its end. For example "wget -O". Any other option can also be placed in
 # the middle.
 #
@@ -20,13 +20,13 @@
 # world, downloading is done much faster in serial, not in parallel. But
 # the project's processing may be done in parallel (with multiple threads
 # needing to download different files at the same time). Therefore, this
-# script uses the `flock' program to only do one download at a time. To
+# script uses the 'flock' program to only do one download at a time. To
 # benefit from it, any call to this script must be given the same lock
 # file. If your system has multiple ports to the internet, or for any
-# reason, you don't want to use a lock file, set the `lockfile' name to
-# `nolock'.
+# reason, you don't want to use a lock file, set the 'lockfile' name to
+# 'nolock'.
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
@@ -114,9 +114,9 @@ while [ ! -f "$outname" ]; do
         sleep $tstep
     fi
 
-    # Attempt downloading the file. Note that the `downloader' ends with
+    # Attempt downloading the file. Note that the 'downloader' ends with
     # the respective option to specify the output name. For example "wget
-    # -O" (so `outname', that comes after it) will be the name of the
+    # -O" (so 'outname', that comes after it) will be the name of the
     # downloaded file.
     if [ x"$lockfile" = xnolock ]; then
         if ! $downloader $outname $inurl; then rm -f $outname; fi
diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf
index fd8ac53..f3d1cd4 100644
--- a/reproduce/analysis/config/INPUTS.conf
+++ b/reproduce/analysis/config/INPUTS.conf
@@ -1,42 +1,70 @@
-# Input files necessary for this project, the variables defined in this
-# file are primarily used in 'reproduce/analysis/make/download.mk'. See
-# there for precise usage of the variables. But comments are also provided
-# here.
-#
-# Necessary variables for each input dataset are listed below. Its good
-# that all the variables of each file have the same base-name (in the
-# example below 'DEMO') with descriptive suffixes, also put a short comment
-# above each group of variables for each dataset, shortly explaining what
-# it is.
-#
-#  1) Local file name ('DEMO-DATA' below): this is the name of the dataset
-#     on the local system (in 'INDIR', given at configuration time). It is
-#     recommended that it be the same name as the online version of the
-#     file like the case here (note how this variable is used in 'DEMO-URL'
-#     for the dataset's full URL). However, this is not always possible, so
-#     the local and server filenames may be different. Ultimately, the file
-#     name is irrelevant, we check the integrity with the checksum.
-#
-#  2) The MD5 checksum of the file ('DEMO-MD5' below): this is very
-#     important for an automatic verification of the file. You can
-#     calculate it by running 'md5sum' on your desired file. You can also
-#     use any other checksum tool that you prefer, just be sure to correct
-#     the respective command in 'reproduce/analysis/make/download.mk'.
-#
-#  3) The human-readable size of the file ('DEMO-SIZE' below): this is an
-#     optional variable, mainly to help a reader of your project get a
-#     sense of the volume they need to download if they don't already have
-#     the dataset. So it is highly recommended to add it (future readers of
-#     your project's source will appreciate it!). You can get it from the
-#     output of 'ls -lh' command on the file. Optionally you can use it in
-#     messages during the configuration phase (when Maneage asks for the
-#     input data directory), along with other info about the file(s).
-#
-#  4) The full dataset URL ('DEMO-URL' below): this is the full URL
-#     (including the file-name) that can be used to download the dataset
-#     when necessary. Also, see the description above on local filename.
-#
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# This project's input file information (metadata).
+#
+# For each input (external) data file that is used within the project,
+# three variables are suggested here (two of them are mandatory). These
+# variables will be used by 'reproduce/analysis/make/download.mk' to import
+# the dataset into the project (within the build directory):
+#
+#   - If the file already exists locally in '$(INDIR)' (the optional input
+#     directory that may have been specified at configuration time with
+#     '--input-dir'), a symbolic link will be added in '$(indir)' (in the
+#     build directory). A symbolic link is used to avoid extra storage when
+#     files are large.
+#
+#   - If the file doesn't exist in '$(INDIR)', or no input directory was
+#     specified at configuration time, then the file is downloaded from a
+#     specific URL.
+#
+# In both cases, before placing the file (or its link) in the build
+# directory, 'reproduce/analysis/make/download.mk' will check the SHA256
+# checksum of the dataset and if it differs from the pre-defined value (set
+# for that file, here), it will abort (since this is not the intended
+# dataset).
+#
+# Therefore, the two variables specifying the URL and SHA256 checksum of
+# the file are MANDATORY. The third variable (INPUT-%-size) showing the
+# human-readable size of the file (from 'ls -lh') is optional (but
+# recommended: because it gives future scientists to get a feeling of the
+# volume of data they need to input: will become important if the
+# size/number of files is large).
+#
+# The naming convension is critical for the input files to be properly
+# imported into the project. In the patterns below, the '%' is the full
+# file name (including its prefix): for example in the demo input of this
+# file in the 'maneage' branch, we have 'INPUT-wfpc2.fits-sha256':
+# therefore, the input file (within the project's '$(indir)') is called
+# 'wfpc2.fits'. This allows you to simply set '$(indir)/wfpc2.fits' as the
+# pre-requisite of any recipe that needs the input file: you will rarely
+# (if at all!) need to use these variables directly.
+#
+#   INPUT-%-sha256: The sha256 checksum of the file. You can generate the
+#                   SHA256 checksum of a file with the 'sha256sum FILENAME'
+#                   command (where 'FILENAME' is the name of your
+#                   file). this is very important for an automatic
+#                   verification of the file: that it hasn't changed
+#                   between different runs of the project (locally or in
+#                   the URL). There are more robust checksum algorithms
+#                   like the 'SHA' standards.
+#
+#   INPUT-%-url: The URL to download the file if it is not available
+#                locally. It can happen that during the first phases of
+#                your project the data aren't yet public. In this case, you
+#                set a phony URL like this (just as a clear place-holder):
+#                'https://this.file/is/not/yet/public'.
+#
+#   INPUT-%-size: The human-readable size of the file (output of 'ls
+#                 -lh'). This is not used by default but can help other
+#                 scientists who would like to run your project get a
+#                 good feeling of the necessary network and storage
+#                 capacity that is necessary to start the project.
+#
+# The input dataset's name (that goes into the '%') can be different from
+# the URL's file name (last component of the URL, after the last '/'). Just
+# note that it is assumed that the local copy (outside of your project) is
+# 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) 2018-2022 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
@@ -48,7 +76,6 @@
 
 
 # Dataset used in this analysis and its checksum for integrity checking.
-MK20DATA = menke20.xlsx
-MK20MD5  = 8e4eee64791f351fec58680126d558a0
-MK20SIZE = 1.9MB
-MK20URL  = https://www.biorxiv.org/content/biorxiv/early/2020/01/18/2020.01.15.908111/DC1/embed/media-1.xlsx
+INPUT-menke20.xlsx-size   = 1.9M
+INPUT-menke20.xlsx-url    = https://www.biorxiv.org/content/biorxiv/early/2020/01/18/2020.01.15.908111/DC1/embed/media-1.xlsx
+INPUT-menke20.xlsx-sha256 = 7839cdc2946134773ffc401cbcc78fb58fc489d2caad65375c85d605b2f8b13e
diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index caac5c9..f570340 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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 015bf2e..a57b529 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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 d96f293..37fc43c 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) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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/demo-plot.mk b/reproduce/analysis/make/demo-plot.mk
index 53e1918..13b0d45 100644
--- a/reproduce/analysis/make/demo-plot.mk
+++ b/reproduce/analysis/make/demo-plot.mk
@@ -1,7 +1,7 @@
 # Second step of analysis:
 #    Data for plot of number/fraction of tools per year.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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 the
@@ -22,16 +22,16 @@
 a2mk20f1c = $(tex-publish-dir)/tools-per-year.txt
 $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
 
-        # Remove the (possibly) produced figure that is created from this
-        # table: it is created by LaTeX's TiKZ package, and includes
-        # multiple files with a fixed prefix.
+#	Remove the (possibly) produced figure that is created from this
+#	table: it is created by LaTeX's TiKZ package, and includes multiple
+#	files with a fixed prefix.
 	rm -f $(tikzdir)/figure-tools-per-year*
 
-        # Write the column metadata in a temporary file name (appending
-        # '.tmp' to the actual target name). Once all steps are done, it is
-        # renamed to the final target. We do this because if there is an
-        # error in the middle, Make will not consider the job to be
-        # complete and will stop here.
+#	Write the column metadata in a temporary file name (appending
+#	'.tmp' to the actual target name). Once all steps are done, it is
+#	renamed to the final target. We do this because if there is an
+#	error in the middle, Make will not consider the job to be complete
+#	and will stop here.
 	echo "# Data of plot showing fraction of papers that mentioned software tools" > $@.tmp
 	echo "# per year to demonstrate the features of Maneage (MANaging data linEAGE)." >> $@.tmp
 	     >> $@.tmp
@@ -48,7 +48,7 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
 	$(call print-general-metadata, $@.tmp)
 
 
-        # Find the maximum number of papers.
+#	Find the maximum number of papers.
 	awk '!/^#/{all[$$1]+=$$2; id[$$1]+=$$3} \
 	     END{ for(year in all) \
 	            printf("%-7d%-10.3f%d\n", year, 100*id[year]/all[year], \
@@ -56,7 +56,7 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
 	        }' $< \
 	    >> $@.tmp
 
-        # Write it into the final target
+#	Write it into the final target
 	mv $@.tmp $@
 
 
@@ -66,15 +66,15 @@ $(a2mk20f1c): $(mk20tab3) | $(tex-publish-dir)
 # Final LaTeX macro
 $(mtexdir)/demo-plot.tex: $(a2mk20f1c) $(pconfdir)/demo-year.conf
 
-        # Find the first year (first column of first row) of data.
+#	Find the first year (first column of first row) of data.
 	v=$$(awk '!/^#/ && c==0{c++; print $$1}' $(a2mk20f1c))
 	echo "\newcommand{\menkefirstyear}{$$v}" > $@
 
-        # Find the number of rows in the plotted table.
+#	Find the number of rows in the plotted table.
 	v=$$(awk '!/^#/{c++} END{print c}' $(a2mk20f1c))
 	echo "\newcommand{\menkenumyears}{$$v}" >> $@
 
-        # Find the number of papers in 1996.
+#	Find the number of papers in 1996.
 	v=$$(awk '$$1==$(menke-demo-year){print $$3}' $(a2mk20f1c))
 	echo "\newcommand{\menkenumpapersdemocount}{$$v}" >> $@
 	echo "\newcommand{\menkenumpapersdemoyear}{$(menke-demo-year)}" >> $@
diff --git a/reproduce/analysis/make/download.mk b/reproduce/analysis/make/download.mk
index ea70fca..7110c8f 100644
--- a/reproduce/analysis/make/download.mk
+++ b/reproduce/analysis/make/download.mk
@@ -5,7 +5,7 @@
 # recipes in this Makefile all use a single file lock to have one download
 # script running at every instant.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -27,70 +27,68 @@
 # Download input data
 # --------------------
 #
-# The input dataset properties are defined in
-# `$(pconfdir)/INPUTS.conf'. For this template we only have one dataset to
-# enable easy processing, so all the extra checks in this rule may seem
-# redundant.
+# 'reproduce/analysis/config/INPUTS.conf' contains the input dataset
+# properties. In most cases, you will not need to edit this rule (or
+# file!). Simply follow the instructions of 'INPUTS.conf' and set the
+# variables names according to the described standards.
 #
-# In a real project, you will need more than one dataset. In that case,
-# just add them to the target list and add an `elif' statement to define it
-# in the recipe.
-#
-# Files in a server usually have very long names, which are mainly designed
-# for helping in data-base management and being generic. Since Make uses
-# file names to identify which rule to execute, and the scope of this
-# research project is much less than the generic survey/dataset, it is
-# easier to have a simple/short name for the input dataset and work with
-# that. In the first condition of the recipe below, we connect the short
-# name with the raw database name of the dataset.
+# TECHNICAL NOTE on the '$(foreach, n ...)' loop of 'inputdatasets': we are
+# using several (relatively complex!) features particular to Make: In GNU
+# Make, '.VARIABLES' "... expands to a list of the names of all global
+# variables defined so far" (from the "Other Special Variables" section of
+# the GNU Make manual). Assuming that the pattern 'INPUT-%-sha256' is only
+# used for input files, we find all the variables that contain the input
+# file name (the '%' is the filename). Finally, using the
+# pattern-substitution function ('patsubst'), we remove the fixed string at
+# the start and end of the variable name.
 #
 # Download lock file: Most systems have a single connection to the
 # internet, therefore downloading is inherently done in series. As a
 # result, when more than one dataset is necessary for download, if they are
 # done in parallel, the speed will be slower than downloading them in
-# series. We thus use the `flock' program to tie/lock the downloading
+# series. We thus use the 'flock' program to tie/lock the downloading
 # process with a file and make sure that only one downloading event is in
 # progress at every moment.
 $(indir):; mkdir $@
 downloadwrapper = $(bashdir)/download-multi-try
-inputdatasets = $(indir)/menke20.xlsx
+inputdatasets = $(foreach i, \
+                  $(patsubst INPUT-%-sha256,%, \
+                    $(filter INPUT-%-sha256,$(.VARIABLES))), \
+                  $(indir)/$(i))
 $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 
-        # Set the necessary parameters for this input file.
-	if   [ $* = menke20.xlsx ]; then
-	  localname=$(MK20DATA); url=$(MK20URL); mdf=$(MK20MD5);
-	else
-	echo; echo; echo "Not recognized input dataset: '$*'."
-	echo; echo; exit 1
-	fi
+#	Set the necessary parameters for this input file as shell variables
+#	(to help in readability).
+	url=$(INPUT-$*-url)
+	sha=$(INPUT-$*-sha256)
 
-        # Download (or make the link to) the input dataset. If the file
-        # exists in `INDIR', it may be a symbolic link to some other place
-        # in the filesystem. To avoid too many links when using these files
-        # during processing, we'll use `readlink -f' so the link we make
-        # here points to the final file directly (note that `readlink' is
-        # part of GNU Coreutils). If its not a link, the `readlink' part
-        # has no effect.
+#	Download (or make the link to) the input dataset. If the file
+#	exists in 'INDIR', it may be a symbolic link to some other place in
+#	the filesystem. To avoid too many links when using these files
+#	during processing, we'll use 'readlink -f' so the link we make here
+#	points to the final file directly (note that 'readlink' is part of
+#	GNU Coreutils). If its not a link, the 'readlink' part has no
+#	effect.
 	unchecked=$@.unchecked
-	if [ -f $(INDIR)/$$localname ]; then
-	  ln -fs $$(readlink -f $(INDIR)/$$localname) $$unchecked
+	if [ -f $(INDIR)/$* ]; then
+	  ln -fs $$(readlink -f $(INDIR)/$*) $$unchecked
 	else
 	  touch $(lockdir)/download
 	  $(downloadwrapper) "wget --no-use-server-timestamps -O" \
 	                     $(lockdir)/download $$url $$unchecked
 	fi
 
-        # Check the md5 sum to see if this is the proper dataset.
-	sum=$$(md5sum $$unchecked | awk '{print $$1}')
-	if [ $$sum = $$mdf ]; then
+#	Check the checksum to see if this is the proper dataset.
+	sum=$$(sha256sum $$unchecked | awk '{print $$1}')
+	if [ $$sum = $$sha ]; then
 	  mv $$unchecked $@
 	  echo "Integrity confirmed, using $@ in this project."
 	else
 	  echo; echo;
-	  echo "Wrong MD5 checksum for input file '$$localname':"
+	  echo "Wrong SHA256 checksum for input file '$*':"
 	  echo "  File location: $$unchecked"; \
-	  echo "  Expected MD5 checksum:   $$mdf"; \
-	  echo "  Calculated MD5 checksum: $$sum"; \
+	  echo "  Expected SHA256 checksum:   $$sha"; \
+	  echo "  Calculated SHA256 checksum: $$sum"; \
 	  echo; exit 1
 	fi
 
@@ -104,7 +102,7 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir)
 # It is very important to mention the address where the data were
 # downloaded in the final report.
 $(mtexdir)/download.tex: $(indir)/menke20.xlsx | $(mtexdir)
-	echo "\newcommand{\menketwentyxlsxname}{$(MK20DATA)}"  > $@
-	echo "\newcommand{\menketwentychecksum}{$(MK20MD5)}"  >> $@
-	echo "\newcommand{\menketwentybytesize}{$(MK20SIZE)}" >> $@
-	echo "\newcommand{\menketwentyurl}{$(MK20URL)}"       >> $@
+	echo "\newcommand{\menketwentyxlsxname}{menke20.xlsx}" > $@
+	echo "\newcommand{\menketwentychecksum}{$(INPUT-menke20.xlsx-sha256)}" >> $@
+	echo "\newcommand{\menketwentybytesize}{$(INPUT-menke20.xlsx-size)}" >> $@
+	echo "\newcommand{\menketwentyurl}{$(INPUT-menke20.xlsx-url)}" >> $@
diff --git a/reproduce/analysis/make/format.mk b/reproduce/analysis/make/format.mk
index fd4060a..979475f 100644
--- a/reproduce/analysis/make/format.mk
+++ b/reproduce/analysis/make/format.mk
@@ -6,7 +6,7 @@
 # because it provides interesting statistics about tools and methods used
 # in scientific papers.
 #
-# Copyright (C) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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 the
@@ -28,13 +28,13 @@ mk20tab3 = $(a1dir)/table-3.txt
 $(a1dir):; mkdir $@
 $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
 
-        # Set a base-name for the table-3 data.
+#	Set a base-name for the table-3 data.
 	base=$(basename $(notdir $<))-table-3
 
-        # Unfortunately XLSX I/O only works when the input and output are
-        # in the directory it is running. So first, we need to switch to
-        # the input directory, run it, then put our desired output where we
-        # want and delete the extra files.
+#	Unfortunately XLSX I/O only works when the input and output are in
+#	the directory it is running. So first, we need to switch to the
+#	input directory, run it, then put our desired output where we want
+#	and delete the extra files.
 	topdir=$$(pwd)
 	cd $(indir)
 	xlsxio_xlsx2csv $(notdir $<)
@@ -42,12 +42,12 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
 	rm $(notdir $<).*.csv
 	cd $$topdir
 
-        # Read the necessary information. Note that we are dealing with a
-        # CSV (comma-separated value) file. But when there are commas in a
-        # string, quotation signs are put around it. The `FPAT' values is
-        # fully described in the GNU AWK manual. In short, it ensures that
-        # if there is a comma in the middle of double-quotes, it doesn't
-        # count as a delimter.
+#	Read the necessary information. Note that we are dealing with a CSV
+#	(comma-separated value) file. But when there are commas in a
+#	string, quotation signs are put around it. The `FPAT' values is
+#	fully described in the GNU AWK manual. In short, it ensures that if
+#	there is a comma in the middle of double-quotes, it doesn't count
+#	as a delimter.
 	echo "# Column 1: YEAR [counter, i16] Year of journal's publication." > $@.tmp
 	echo "# Column 2: NUM_PAPERS [counter, i16] Number of studied papers in that journal." >> $@.tmp
 	echo "# Column 3: NUM_PAPERS_WITH_TOOLS [counter, i16] Number of papers with an identified tool." >> $@.tmp
@@ -56,9 +56,9 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
 	awk 'NR>1{printf("%-10d%-10d%-10d%-10d %s\n", $$2, $$3, $$3*$$NF, $$(NF-1), $$1)}' \
 	    FPAT='([^,]+)|("[^"]+")' $(indir)/$$base.csv >> $@.tmp
 
-        # Set the temporary file as the final target. This was done so if
-        # there is any possible crash in the steps above, this rule is
-        # re-run (its final target isn't rebuilt).
+#	Set the temporary file as the final target. This was done so if
+#	there is any possible crash in the steps above, this rule is re-run
+#	(its final target isn't rebuilt).
 	mv $@.tmp $@
 
 
@@ -68,19 +68,19 @@ $(mk20tab3): $(indir)/menke20.xlsx | $(a1dir)
 # Main LaTeX macro file
 $(mtexdir)/format.tex: $(mk20tab3)
 
-        # Count the total number of papers in their study.
+#	Count the total number of papers in their study.
 	v=$$(awk '!/^#/{c+=$$2} END{print c}' $(mk20tab3))
 	echo "\newcommand{\menkenumpapers}{$$v}" > $@
 
-        # Count how many unique journals there were in the study. Note that
-        # the `31' comes because we put 10 characters for each numeric
-        # column and separated the last numeric column from the string
-        # column with a space. If the number of numeric columns change in
-        # the future, the `31' also has to change.
+#	Count how many unique journals there were in the study. Note that
+#	the `31' comes because we put 10 characters for each numeric column
+#	and separated the last numeric column from the string column with a
+#	space. If the number of numeric columns change in the future, the
+#	`31' also has to change.
 	v=$$(awk 'BEGIN{FIELDWIDTHS="41 10000"} !/^#/{print $$2}' \
 	         $(mk20tab3) | uniq | wc -l)
 	echo "\newcommand{\menkenumjournals}{$$v}" >> $@
 
-        # Count how many rows the original catalog has.
+#	Count how many rows the original catalog has.
 	v=$$(awk '!/^#/{c++} END{print c}' $(mk20tab3))
 	echo "\newcommand{\menkenumorigrows}{$$v}" >> $@
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index bc73df8..7f0c514 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
 # Project initialization.
 #
-# Copyright (C) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This Makefile is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -25,10 +25,10 @@
 # Basic directories that are used throughout the project.
 #
 # Locks are used to make sure that an operation is done in series not in
-# parallel (even if Make is run in parallel with the `-j' option). The most
+# parallel (even if Make is run in parallel with the '-j' option). The most
 # common case is downloads which are better done in series and not in
 # parallel. Also, some programs may not be thread-safe, therefore it will
-# be necessary to put a lock on them. This project uses the `flock' program
+# be necessary to put a lock on them. This project uses the 'flock' program
 # to achieve this.
 #
 # To help with modularity and clarity of the build directory (not mixing
@@ -43,7 +43,7 @@ bsdir=$(BDIR)/software
 texdir      = $(badir)/tex
 lockdir     = $(bsdir)/locks
 indir       = $(badir)/inputs
-prepdir     = $(padir)/prepare
+prepdir     = $(badir)/prepare
 mtexdir     = $(texdir)/macros
 installdir  = $(bsdir)/installed
 bashdir     = reproduce/analysis/bash
@@ -56,10 +56,10 @@ pconfdir    = reproduce/analysis/config
 # Preparation phase
 # -----------------
 #
-# This Makefile is loaded both for the `prepare' phase and the `make'
+# This Makefile is loaded both for the 'prepare' phase and the 'make'
 # phase. But the preparation files should be dealt with differently
-# (depending on the phase). In the `prepare' phase, the main directory
-# should be created, and in the `make' phase, its contents should be
+# (depending on the phase). In the 'prepare' phase, the main directory
+# should be created, and in the 'make' phase, its contents should be
 # loaded.
 #
 # If you don't need any preparation, please simply comment these lines.
@@ -87,6 +87,14 @@ endif
 # (independent parts of the paper can be added to it independently). To fix
 # this problem, when we are in a group setting, we'll use the user's ID to
 # create a separate LaTeX build directory for each user.
+#
+# The same logic applies to the final paper PDF: each user will create a
+# separte final PDF (for example 'paper-user1.pdf' and 'paper-user2.pdf')
+# and no 'paper.pdf' will be built. This isn't a problem because
+# 'initialize.tex' is a .PHONY prerequisite, so the rule to build the final
+# paper is always executed (even if it is present and nothing has
+# changed). So in terms of over-all efficiency and processing steps, this
+# doesn't change anything.
 ifeq (x$(GROUP-NAME),x)
 texbtopdir  = build
 else
@@ -104,7 +112,7 @@ tikzdir     = $(texbdir)/tikz
 # ---------------------------
 #
 # Before defining the local sub-environment here, we'll need to save the
-# system's environment for some scenarios (for example after `clean'ing the
+# system's environment for some scenarios (for example after 'clean'ing the
 # built programs).
 curdir   := $(shell echo $$(pwd))
 
@@ -117,16 +125,16 @@ curdir   := $(shell echo $$(pwd))
 #
 # We want the full recipe to be executed in one call to the shell. Also we
 # want Make to run the specific version of Bash that we have installed
-# during `./project configure' time.
+# during './project configure' time.
 #
 # Regarding the directories, this project builds its major dependencies
 # itself and doesn't use the local system's default tools. With these
 # environment variables, we are setting it to prefer the software we have
 # build here.
 #
-# `TEXINPUTS': we have to remove all possible user-specified directories to
-# avoid conflicts with existing TeX Live solutions. Later (in `paper.mk'),
-# we are also going to overwrite `TEXINPUTS' just before `pdflatex'.
+# 'TEXINPUTS': we have to remove all possible user-specified directories to
+# avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'),
+# we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'.
 .ONESHELL:
 .SHELLFLAGS = -ec
 export TERM=xterm
@@ -144,12 +152,12 @@ export LD_LIBRARY_PATH := $(installdir)/lib
 # will be empty.
 export CPATH := $(SYS_CPATH)
 
-# RPATH is automatically written in macOS, so `DYLD_LIBRARY_PATH' is
+# RPATH is automatically written in macOS, so 'DYLD_LIBRARY_PATH' is
 # ultimately redundant. But on some systems, even having a single value
 # causes crashs (see bug #56682). So we'll just give it no value at all.
 export DYLD_LIBRARY_PATH :=
 
-# OpenMPI can depend on an existing `ssh' or `rsh' binary. However, because
+# OpenMPI can depend on an existing 'ssh' or 'rsh' binary. However, because
 # of security reasons, its best to not install them, disable any
 # remote-shell accesss through this environment variable.
 export OMPI_MCA_plm_rsh_agent=/bin/false
@@ -163,7 +171,7 @@ export BASH_ENV := $(shell pwd)/reproduce/software/shell/bashrc.sh
 # Python enviroment
 # -----------------
 #
-# The main Python environment variable is `PYTHONPATH'. However, so far we
+# The main Python environment variable is 'PYTHONPATH'. However, so far we
 # have found several other Python-related environment variables on some
 # systems which might interfere. To be safe, we are removing all their
 # values.
@@ -187,10 +195,10 @@ export MPI_PYTHON3_SITEARCH   :=
 # directories (or possible sub-directories) for individual steps will be
 # defined and added within their own Makefiles.
 #
-# The `.SUFFIXES' rule with no prerequisite is defined to eliminate all the
+# The '.SUFFIXES' rule with no prerequisite is defined to eliminate all the
 # default implicit rules. The default implicit rules are to do with
-# programming (for example converting `.c' files to `.o' files). The
-# problem they cause is when you want to debug the make command with `-d'
+# programming (for example converting '.c' files to '.o' files). The
+# problem they cause is when you want to debug the make command with '-d'
 # option: they add too many extra checks that make it hard to find what you
 # are looking for in the outputs.
 .SUFFIXES:
@@ -201,8 +209,11 @@ $(lockdir): | $(bsdir); mkdir $@
 
 
 # Version and distribution tarball definitions
-project-commit-hash := $(shell if [ -d .git ]; then \
-    echo $$(git describe --dirty --always --long); else echo NOGIT; fi)
+project-commit-hash := $(shell \
+    if [ -d .git ]; then \
+      export LD_LIBRARY_PATH="$(installdir)/lib"; \
+      echo $$($(installdir)/bin/git describe --dirty --always --long); \
+    else echo NOGIT; fi)
 project-package-name := maneaged-$(project-commit-hash)
 project-package-contents = $(texdir)/$(project-package-name)
 
@@ -213,10 +224,10 @@ project-package-contents = $(texdir)/$(project-package-name)
 # High-level Makefile management
 # ------------------------------
 #
-# About `.PHONY': these are targets that must be built even if a file with
+# About '.PHONY': these are targets that must be built even if a file with
 # their name exists.
 #
-# Only `$(mtexdir)/initialize.tex' corresponds to a file. This is because
+# Only '$(mtexdir)/initialize.tex' corresponds to a file. This is because
 # we want to ensure that the file is always built in every run: it contains
 # the project version which may change between two separate runs, even when
 # no file actually differs.
@@ -229,14 +240,20 @@ texclean:
 	mkdir $(texdir)/build/tikz # 'tikz' is assumed to already exist.
 
 clean:
-        # Delete the top-level PDF file.
+#	Delete the top-level PDF file.
 	rm -f *.pdf
 
-        # 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.
+#	Delete possible LaTeX output in top directory. This can happen when
+#	the user has run LaTeX with applications other than maneage. For
+#	example, when opening 'paper.tex' file with 'texstudio' and
+#	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))
@@ -244,14 +261,13 @@ clean:
 	rm -rf $(bsdir)/preparation-done.mk
 
 distclean: clean
-        #  Without cleaning the Git hooks, we won't be able to easily
-        #  commit or checkout after this task is done. So we'll remove them
-        #  first.
+#	Without cleaning the Git hooks, we won't be able to easily commit
+#	or checkout after this task is done. So we'll remove them first.
 	rm -f .git/hooks/post-checkout .git/hooks/pre-commit
 
-        # We'll be deleting the built environent programs and just need the
-        # `rm' program. So for this recipe, we'll use the host system's
-        # `rm', not our own.
+#	We'll be deleting the built environent programs and just need the
+#	'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
 
@@ -268,15 +284,15 @@ distclean: clean
 # without having to worry about the technicalities of the analysis.
 $(project-package-contents): paper.pdf | $(texdir)
 
-        # Set up the output directory, delete it if it exists and remake it
-        # to fill with new contents.
+#	Set up the output directory, delete it if it exists and remake it
+#	to fill with new contents.
 	dir=$@
 	rm -rf $$dir
 	mkdir $$dir
 	curdir=$$(pwd)
 
-        # Build a small Makefile to help in automatizing the paper building
-        # (including the bibliography).
+#	Build a small Makefile to help in automatizing the paper building
+#	(including the bibliography).
 	m=$$dir/Makefile
 	echo   "paper.pdf: paper.tex paper.bbl"                   > $$m
 	printf "\tlatex -shell-escape -halt-on-error paper\n"    >> $$m
@@ -291,94 +307,92 @@ $(project-package-contents): paper.pdf | $(texdir)
 	printf "\trm -f *.aux *.auxlock *.bbl *.bcf\n"           >> $$m
 	printf "\trm -f *.blg *.log *.out *.run.xml\n"           >> $$m
 
-        # Copy the top-level contents (see next step for `paper.tex').
+#	Copy the top-level contents (see next step for 'paper.tex').
 	cp COPYING project README.md README-hacking.md $$dir/
 
-        # Since the packaging is mainly intended for high-level building of
-        # the PDF with LaTeX, we'll comment the `makepdf' LaTeX macro in
-        # the paper. This will disable usage of TiKZ.
+#	Since the packaging is mainly intended for high-level building of
+#	the PDF with LaTeX, we'll comment the 'makepdf' LaTeX macro in the
+#	paper. This will disable usage of TiKZ.
 	sed -e's|\\newcommand{\\makepdf}{}|%\\newcommand{\\makepdf}{}|' \
 	    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).
-        #
-        # To keep the sub-directory structure, we are packaging the files
-        # with Tar, piping it, and unpacking it in the archive
-        # directory. So afterwards we need to come back to the current
-        # directory.
+#	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).
+#
+#	To keep the sub-directory structure, we are packaging the files
+#	with Tar, piping it, and unpacking it in the archive directory. So
+#	afterwards we need to come back to the current directory.
 	tar -c -f - $$(git ls-files peer-review reproduce tex/src) \
 	    | (cd $$dir ; tar -x -f -)
 	cd $(curdir)
 
-        # Build the other two subdirectories of 'tex/' that we need in the
-        # archive (in the actual project, these are symbolic links to the
-        # build directory).
+#	Build the other two subdirectories of 'tex/' that we need in the
+#	archive (in the actual project, these are symbolic links to the
+#	build directory).
 	mkdir $$dir/tex/tikz $$dir/tex/build
 
-        # Copy the 'tex/build' directory into the archive (excluding the
-        # temporary archive directory that we are now copying to). We will
-        # be using Bash's extended globbing ('extglob') for excluding this
-        # directory.
+#	Copy the 'tex/build' directory into the archive (excluding the
+#	temporary archive directory that we are now copying to). We will be
+#	using Bash's extended globbing ('extglob') for excluding this
+#	directory.
 	shopt -s extglob
 	cp -r tex/img                              $$dir/tex/img
 	cp tex/tikz/*.eps                          $$dir/tex/tikz
 	cp -r tex/build/!($(project-package-name)) $$dir/tex/build
 
-        # Clean up the $(texdir)/build* directories in the archive (when
-        # building in a group structure, there will be `build-user1',
-        # `build-user2' and etc). These are just temporary LaTeX build
-        # files and don't have any relevant/hand-written files in them.
+#	Clean up the $(texdir)/build* directories in the archive (when
+#	building in a group structure, there will be 'build-user1',
+#	'build-user2' and etc). These are just temporary LaTeX build files
+#	and don't have any relevant/hand-written files in them.
 	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.
+#	If the project has any PDFs in its 'tex/tikz' directory (TiKZ or
+#	PGFPlots was used to generate them), copy them too.
 	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 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 use the same strategy for other LaTeX packages
-        # that may cause problems on the arXiv server.
+#	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
+#	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
+#	use the same strategy for other LaTeX packages that may cause
+#	problems on the arXiv server.
 	cp tex/build/build/paper.bbl $$dir/
 	tltopdir=.local/texlive/maneage/texmf-dist/tex/latex
         #find $$tltopdir/biblatex/ -maxdepth 1 -type f -print0 \
         #     | xargs -0 cp -t $$dir
 
-        # Just in case the package users want to rebuild some of the
-        # figures (manually un-comment the `makepdf' command we commented
-        # above), correct the TikZ external directory, so the figures can
-        # be rebuilt.
+#	Just in case the package users want to rebuild some of the figures
+#	(manually un-comment the 'makepdf' command we commented above),
+#	correct the TikZ external directory, so the figures can be rebuilt.
 	pgfsettings="$$dir/tex/src/preamble-pgfplots.tex"
 	sed -e's|{tikz/}|{tex/tikz/}|' $$pgfsettings > $$pgfsettings.new
 	mv $$pgfsettings.new $$pgfsettings
 
-        # PROJECT SPECIFIC
-        # ----------------
-        # Put any project-specific distribution steps here.
+#	PROJECT SPECIFIC
+#	----------------
+#	Put any project-specific distribution steps here.
 	cd $$curdir
 	cp tex/build/build/appendix.bbl $$dir/
-        # ----------------
+#	----------------
 
-        # Clean temporary files that may have been created by text editors.
+#	Clean temporary files that may have been created by text editors.
 	cd $(texdir)
 	find $(project-package-name) -name \*~ -delete
 	find $(project-package-name) -name \*.swp -delete
 
-# Package into `.tar.gz' or '.tar.lz'.
+# Package into '.tar.gz' or '.tar.lz'.
 dist dist-lzip: $(project-package-contents)
 	curdir=$$(pwd)
 	cd $(texdir)
@@ -394,7 +408,7 @@ dist dist-lzip: $(project-package-contents)
 	cd $$curdir
 	mv $(texdir)/$(project-package-name).tar.$$suffix ./
 
-# Package into `.zip'.
+# Package into '.zip'.
 dist-zip: $(project-package-contents)
 	curdir=$$(pwd)
 	cd $(texdir)
@@ -495,13 +509,13 @@ print-general-metadata = \
 # This file will store some basic info about the project that is necessary
 # for the final PDF. Since these are not version controlled, it must be
 # calculated everytime the project is run. So even though this file
-# actually exists, it is also aded as a `.PHONY' target above.
+# actually exists, it is also aded as a '.PHONY' target above.
 $(mtexdir)/initialize.tex: | $(mtexdir)
 
-        # Version and title of project. About the starting '@': since these
-        # commands are run every time with './project make', it is annoying
-        # to print them on the standard output every time. With the '@',
-        # make will not print the commands that it runs in this recipe.
+#	Version and title of project. About the starting '@': since these
+#	commands are run every time with './project make', it is annoying
+#	to print them on the standard output every time. With the '@', make
+#	will not print the commands that it runs in this recipe.
 	@d=$$(git show -s --format=%aD HEAD | awk '{print $$2, $$3, $$4}')
 	echo "\newcommand{\projectdate}{$$d}" > $@
 	echo "\newcommand{\projecttitle}{$(metadata-title)}" >> $@
@@ -514,16 +528,15 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
 	v=$$(echo $(metadata-doi-zenodo) | sed -e's/\./ /g' | awk '{print $$NF}')
 	echo "\newcommand{\projectzenodoid}{$$v}" >> $@
 
-        # Calculate the latest Maneage commit used to build this
-        # project:
-        #  - The project may not have the 'maneage' branch (for example
-        #    after cloning from a fork that didn't include it!). In this
-        #    case, we'll print a descriptive warning, telling the user what
-        #    should be done (reporting the last merged commit and its date
-        #    is very useful for the future).
-        #  - The '--dirty' option (used in 'project-commit-hash') isn't
-        #    applicable to "commit-ishes" (direct quote from Git's error
-        #    message!).
+#	Calculate the latest Maneage commit used to build this project:
+#	  - The project may not have the 'maneage' branch (for example
+#	    after cloning from a fork that didn't include it!). In this
+#	    case, we'll print a descriptive warning, telling the user what
+#	    should be done (reporting the last merged commit and its date
+#	    is very useful for the future).
+#	  - The '--dirty' option (used in 'project-commit-hash') isn't
+#	    applicable to "commit-ishes" (direct quote from Git's error
+#	    message!).
 	if git log maneage -1 &> /dev/null; then
 	  c=$$(git merge-base HEAD maneage)
 	  v=$$(git describe --always --long $$c)
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 00bd3b5..da2702c 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -24,14 +24,14 @@
 #
 # To report the input settings and results, the final report's PDF (final
 # target of this project) uses macros generated from various steps of the
-# project. All these macros are defined through `$(mtexdir)/project.tex'.
+# project. All these macros are defined through '$(mtexdir)/project.tex'.
 #
-# `$(mtexdir)/project.tex' is actually just a combination of separate files
+# '$(mtexdir)/project.tex' is actually just a combination of separate files
 # that keep the LaTeX macros related to each workhorse Makefile (in
-# `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
-# `$(mtexdir)/verify.tex' which will check them before starting to build
+# 'reproduce/src/make/*.mk'). Those individual macros are pre-requisites to
+# '$(mtexdir)/verify.tex' which will check them before starting to build
 # the paper. The only workhorse Makefile that doesn't need to produce LaTeX
-# macros is this Makefile (`reproduce/src/make/paper.mk').
+# macros is this Makefile ('reproduce/src/make/paper.mk').
 #
 # This file is thus the interface between the analysis/processing steps and
 # the final PDF: when we get to this point, all the processing has been
@@ -39,38 +39,38 @@
 #
 # Note that if you don't want the final PDF and just want the processing
 # and file outputs, you can give any value other than 'yes' to
-# 'pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
 $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 
-        # If no PDF is requested, or if LaTeX isn't available, don't
-        # continue to building the final PDF. Otherwise, merge all the TeX
-        # macros into one for building the PDF.
+#	If no PDF is requested, or if LaTeX isn't available, don't continue
+#	to building the final PDF. Otherwise, merge all the TeX macros into
+#	one for building the PDF.
 	@if [ -f .local/bin/latex ] && [ x"$(pdf-build-final)" = xyes ]; then
 
-          # Put a LaTeX input command for all the necessary macro files.
-          # 'hardware-parameters.tex' is created in 'configure.sh'.
+#	  Put a LaTeX input command for all the necessary macro files.
+#	  'hardware-parameters.tex' is created in 'configure.sh'.
 	  projecttex=$(mtexdir)/project.tex
 	  rm -f $$projecttex
 	  for t in $(subst paper,,$(makesrc)) hardware-parameters; do
 	    echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex
 	  done
 
-          # Possibly print the appendix in the final PDF.
+#	  Possibly print the appendix in the final PDF.
 	  if [ x"$(separatesupplement)" = x1 ]; then
 	    echo "\newcommand{\separatesupplement}{}" >> $$projecttex
 	  fi
 
-          # Possibly highlight the '\new' parts of the text.
+#	  Possibly highlight the '\new' parts of the text.
 	  if [ x"$(highlightnew)" = x1 ]; then
 	    echo "\newcommand{\highlightnew}{}" >> $$projecttex
 	  fi
 
-          # Possibly show the text within '\tonote'.
+#	  Possibly show the text within '\tonote'.
 	  if [ x"$(highlightnotes)" = x1 ]; then
 	    echo "\newcommand{\highlightnotes}{}" >> $$projecttex
 	  fi
 
-        # The paper shouldn't be built.
+#	The paper shouldn't be built.
 	else
 	  echo
 	  echo "-----"
@@ -101,76 +101,76 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex
 # The bibliography
 # ----------------
 #
-# We need to run the `bibtex' program on the output of LaTeX to generate
+# We need to run the 'bibtex' program on the output of LaTeX to generate
 # the necessary bibliography before making the final paper. So we'll first
-# have one run of LaTeX (similar to the `paper.pdf' recipe), then `biber'.
+# have one run of LaTeX (similar to the 'paper.pdf' recipe), then 'bibtex'.
 #
-# NOTE: `$(mtexdir)/project.tex' is an order-only-prerequisite for
-# `paper.bbl'. This is because we need to run LaTeX in both the `paper.bbl'
-# recipe and the `paper.pdf' recipe. But if `tex/src/references.bib' hasn't
+# NOTE: '$(mtexdir)/project.tex' is an order-only-prerequisite for
+# 'paper.bbl'. This is because we need to run LaTeX in both the 'paper.bbl'
+# recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't
 # been modified, we don't want to re-build the bibliography, only the final
 # PDF.
 bbls = $(foreach t,$(subst .pdf,,$(top-pdfs)),$(texbdir)/$(t).bbl)
 $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
          $(mtexdir)/dependencies-bib.tex | $(mtexdir)/project.tex
 
-        # If `$(mtexdir)/project.tex' is empty, don't build PDF.
+#	If '$(mtexdir)/project.tex' is empty, don't build PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
 
-          # Unfortunately I can't get bibtex to look into a special
-          # directory for the references, so we'll copy it into the LaTeX
-          # building directory.
+#	  Unfortunately I can't get bibtex to look into a special directory
+#	  for the references, so we'll copy it into the LaTeX building
+#	  directory.
 	  p=$$(pwd)
 	  if ! [ -L $(texbdir)/references.bib ]; then
 	    ln -sf $$p/tex/src/references.tex $(texbdir)/references.bib
 	  fi
 
-          # Copy the improved IEEE bst file into the build directory.
-          # The improved bst file provides ArXiv clickable URLs and
-          # if available, open-access URLs based on the DOIs, with
-          # closed-access URLs as a fallback, via https://oadoi.org .
+#	  Copy the improved IEEE bst file into the build directory. The
+#	  improved bst file provides ArXiv clickable URLs and if available,
+#	  open-access URLs based on the DOIs, with closed-access URLs as a
+#	  fallback, via https://oadoi.org .
 	  ln -sf $$p/tex/src/IEEEtran_openaccess.bst $(texbdir)/
 
-          # We'll run LaTeX first to generate the `.bcf' file (necessary
-          # for `biber') and then run `biber' to generate the `.bbl' file.
+#	  We'll run LaTeX first to generate the '.bcf' file (necessary for
+#	  'bibtex') and then run 'bibtex' to generate the '.bbl' file.
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir);
 
-          # Delete any possibly existing target (a '.bbl' file) to avoid
-          # complications with LaTeX being run before the command that
-          # generates it. Otherwise users will have to manually delete
-          # it. It will be built anyway once this rule is done.
+#	  Delete any possibly existing target (a '.bbl' file) to avoid
+#	  complications with LaTeX being run before the command that
+#	  generates it. Otherwise users will have to manually delete it. It
+#	  will be built anyway once this rule is done.
 	  rm -f $@
 
-          # Put a link to the main LaTeX source that we want to build.
+#	  Put a link to the main LaTeX source that we want to build.
 	  if [ $* = paper ]; then sdir="$$p"
 	  else                    sdir="$$p"/tex/src
 	  fi
 	  ln -sf "$$sdir"/$*.tex ./
 
-          # The pdflatex option '-shell-escape' is "normally disallowed for
-          # security reasons" according to the `info pdflatex' manual, but
-          # is enabled here in order to allow the use of PGFPlots. If you
-          # do not use PGFPlots, then you can remove the `-shell-escape'
-          # option for better security. See
-          # https://savannah.nongnu.org/task/?15694 for details.
+#	  The pdflatex option '-shell-escape' is "normally disallowed for
+#	  security reasons" according to the 'info pdflatex' manual, but is
+#	  enabled here in order to allow the use of PGFPlots. If you do not
+#	  use PGFPlots, then you should remove the '-shell-escape' option
+#	  for better security. See https://savannah.nongnu.org/task/?15694
+#	  for details.
 	  latex -shell-escape -halt-on-error $*.tex
 
-          # When we are building the main paper and the appendices are to
-          # be built within the main paper's PDF, we need two
-          # bibliographies: one for the main body, and one for the
-          # appendix. For this, we use 'multibib'. Multibib creates a
-          # separate '.aux' file for each bibliography.
+#	  When we are building the main paper and the appendices are to be
+#	  built within the main paper's PDF, we need two bibliographies:
+#	  one for the main body, and one for the appendix. For this, we use
+#	  'multibib'. Multibib creates a separate '.aux' file for each
+#	  bibliography.
 	  bibtex $*
 	  if [ x"$(separatesupplement)" != x1 ]; then
 	    bibtex appendix
 	  fi
 
-          # Hack: tidy up eprint+doi style that didn't work in .bst file.
-          # TODO (better): read Part 4 of
-          # http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf
-          # and fix the .bst style properly.
+#	  Hack: tidy up eprint+doi style that didn't work in .bst file.
+#	  TODO (better): read Part 4 of
+#	  http://mirrors.ctan.org/info/bibtex/tamethebeast/ttb_en.pdf and
+#	  fix the .bst style properly.
 	  cp -pv $*.bbl $*-tmp.bbl \
 	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
@@ -188,7 +188,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 	      | sed -e 's/EOLINE/\n/g' > appendix.bbl
 	  fi
 
-	  # Paper-specific hacks for reducing very-long author lists.
+#	  Paper-specific hacks for reducing very-long author lists.
 	  cp -pv $*.bbl $*-tmp.bbl \
 	    && sed -e "s/\'/EOLINE/g" $*-tmp.bbl \
 	    | tr -d '\n' \
@@ -196,7 +196,7 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 	    | sed -e 's;, V\..Khodiyar[^{]*Whyte; et al.\\/;' \
 	    | sed -e 's/EOLINE/\n/g' > $*.bbl
 
-          # The pre-final run of LaTeX after 'paper.bbl' was created.
+#	  The pre-final run of LaTeX after 'paper.bbl' was created.
 	  latex -shell-escape -halt-on-error $*.tex
 	fi
 
@@ -207,36 +207,36 @@ $(bbls): $(texbdir)/%.bbl: tex/src/references.tex \
 # The final paper
 # ---------------
 #
-# Run LaTeX in the `$(texbdir)' directory so all the intermediate and
+# Run LaTeX in the '$(texbdir)' directory so all the intermediate and
 # auxiliary files stay there and keep the top directory clean. To be able
 # to run everything cleanly from there, it is necessary to add the current
-# directory (top project directory) to the `TEXINPUTS' environment
+# directory (top project directory) to the 'TEXINPUTS' environment
 # variable.
 $(top-pdfs): %.pdf: $(mtexdir)/project.tex paper.tex \
          tex/src/appendix-*.tex $(texbdir)/%.bbl
 
-        # If `$(mtexdir)/project.tex' is empty, don't build the PDF.
+#	If '$(mtexdir)/project.tex' is empty, don't build the PDF.
 	@macros=$$(cat $(mtexdir)/project.tex)
 	if [ x"$$macros" != x ]; then
 
-          # Go into the top TeX build directory and make the paper.
+#	  Go into the top TeX build directory and make the paper.
 	  p=$$(pwd)
 	  export TEXINPUTS=$$p:
 	  cd $(texbdir)
 
-          # See above for a warning and brief discussion on the the
-          # pdflatex option `-shell-escape'.
+#	  See above for a warning and brief discussion on the the pdflatex
+#	  option '-shell-escape'.
 	  latex -shell-escape -halt-on-error $*.tex
 
-          # Convert the DVI to PostScript, and the PostScript to PDF. The
-          # `-dNOSAFER' option to GhostScript allows transparencies in the
-          # conversion from PostScript to PDF, see
-          # https://www.ghostscript.com/doc/current/Language.htm#Transparency
+#	  Convert the DVI to PostScript, and the PostScript to PDF. The
+#	  '-dNOSAFER' option to GhostScript allows transparencies in the
+#	  conversion from PostScript to PDF, see
+#	  https://www.ghostscript.com/doc/current/Language.htm#Transparency
 	  dvips $*.dvi
 	  ps2pdf $*.ps
 
-          # Come back to the top project directory and copy the built PDF
-          # file here.
+#	  Come back to the top project directory and copy the built PDF
+#	  file here.
 	  cd "$$p"
 	  cp $(texbdir)/$*.pdf $@
 	fi
diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk
index d0b61d9..ecb6842 100644
--- a/reproduce/analysis/make/prepare.mk
+++ b/reproduce/analysis/make/prepare.mk
@@ -1,6 +1,6 @@
-# Basic preparations, called by `./project prepare'.
+# Basic preparations, called by './project prepare'.
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
@@ -21,30 +21,29 @@
 
 # Final-target
 #
-# Without this file, `./project make' won't work.
+# Without this file, './project make' won't work.
 prepare-dep = $(subst prepare, ,$(makesrc))
 $(bsdir)/preparation-done.mk: \
                 $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex)
 
-        # If you need to add preparations define targets above to do the
-        # preparations, then set the value below to `yes'. Recall that just
-        # like `./project make', before loading this file, `./project
-        # prepare' loads loads `initialize.mk' and `download.mk', so you
-        # can safely assume everything that is defined there in the
-        # preparation phase also.
-        #
-        # TIP: the targets can actually be automatically generated
-        # Makefiles that are used by `./project make'. They can include
-        # variables, or automatically generated rules. Just make sure that
-        # those Makefiles aren't written in the source directory. Even
-        # though they are Makefiles, they are automatically built, so they
-        # don't belong in the source. `$(prepdir)' has been defined for
-        # this purpose (see `initialize.mk'), we recommend that you put all
-        # automatically generated Makefiles under this directory. In the
-        # `make' phase, `initialize.mk' will automatically load all the
-        # `*.mk' files. If you need to load your generated
-        # configuration-makefiles before automatically generated Makefiles
-        # containing rules, you can use some naming convension like
-        # `conf-*.mk' and `rule-*.mk', or you can put them in
-        # subdirectories.
+#	If you need to add preparations define targets above to do the
+#	preparations, then set the value below to 'yes'. Recall that just
+#	like './project make', before loading this file, './project
+#	prepare' loads loads 'initialize.mk' and 'download.mk', so you can
+#	safely assume everything that is defined there in the preparation
+#	phase also.
+#
+#	TIP: the targets can actually be automatically generated Makefiles
+#	that are used by './project make'. They can include variables, or
+#	automatically generated rules. Just make sure that those Makefiles
+#	aren't written in the source directory. Even though they are
+#	Makefiles, they are automatically built, so they don't belong in
+#	the source. '$(prepdir)' has been defined for this purpose (see
+#	'initialize.mk'), we recommend that you put all automatically
+#	generated Makefiles under this directory. In the 'make' phase,
+#	'initialize.mk' will automatically load all the '*.mk' files. If
+#	you need to load your generated configuration-makefiles before
+#	automatically generated Makefiles containing rules, you can use
+#	some naming convension like 'conf-*.mk' and 'rule-*.mk', or you can
+#	put them in subdirectories.
 	@echo "include-prepare-results = no" > $@
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 27c1b5b..7755174 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) 2018-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2022 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
@@ -20,7 +20,7 @@
 
 
 # Load the local configuration (created after running
-# `./project configure').
+# './project configure').
 include reproduce/software/config/LOCAL.conf
 
 
@@ -30,7 +30,7 @@ include reproduce/software/config/LOCAL.conf
 # Ultimate target of this project
 # -------------------------------
 #
-# The final paper/report (`paper.pdf') is the main target of this
+# The final paper/report ('paper.pdf') is the main target of this
 # project. As defined in the Make paradigm, it must be the first target
 # that Make encounters (immediately after loading the local configuration
 # settings, necessary for a group building scenario mentioned next).
@@ -50,8 +50,8 @@ include reproduce/software/config/LOCAL.conf
 #
 # Controlling this requires two variables that are available at this stage:
 #
-#   - `GROUP-NAME': from `LOCAL.conf' (which was built by `./project configure').
-#   - `maneage_group_name': value to the `--group' option.
+#   - 'GROUP-NAME': from 'LOCAL.conf' (which was built by './project configure').
+#   - 'maneage_group_name': value to the '--group' option.
 #
 # The analysis is only done when both have the same group name. Note that
 # when the project isn't being built for a group, both variables will be an
@@ -63,7 +63,7 @@ include reproduce/software/config/LOCAL.conf
 #
 # If you are just interested in the processing and don't want to build the
 # PDF, you can skip the creation of the final PDF by giving a value of
-# `yes' to `pdf-build-final' in `reproduce/analysis/config/pdf-build.conf'.
+# 'yes' to 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'.
 ifeq ($(separatesupplement),0)
 top-pdfs = paper.pdf
 else
@@ -92,13 +92,13 @@ endif
 # To keep things clean, managable and readable, each set of operations
 # is (and must be) classified (modularized) by context into separate
 # Makefiles: the more the better. These modular steps are then
-# included in this top-level Makefile through the `include' command of
+# included in this top-level Makefile through the 'include' command of
 # the next step. Each Makefile should also produce a LaTeX macro file
 # with the same fixed name (used to keep all the parameters and
 # relevant outputs of the steps in it for the final paper).
 #
 # In the rare case that no special LaTeX macros are necessary in a
-# workhorse Makefile, you can simply make an empty file with `touch
+# workhorse Makefile, you can simply make an empty file with 'touch
 # $@'. This will not add any lines to the final combined LaTeX macros
 # file, but will create the file that is a prerequisite to the final
 # paper generation.
@@ -112,7 +112,7 @@ endif
 # IMPORTANT NOTE: order matters in the inclusion of the processing
 # Makefiles. As the project grows, some Makefiles will define
 # variables/dependencies that later Makefiles need. Therefore we are using
-# a `foreach' loop in the next step to explicitly request loading them in
+# a 'foreach' loop in the next step to explicitly request loading them in
 # the same order that they are defined here (we aren't just using a
 # wild-card like the configuration Makefiles).
 makesrc = initialize \
@@ -136,7 +136,7 @@ makesrc = initialize \
 #      contain rules to actually do this project's processing.
 #
 # But before that, we need to identify the phase for the Makefiles that are
-# run both in `./project prepare' and `./project make'.
+# run both in './project prepare' and './project make'.
 project-phase = make
 include reproduce/analysis/config/*.conf
 include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index fb5700e..3950bf1 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -1,10 +1,10 @@
 # Do basic preparations to optimize the project's running.
 #
-# NOTE: This file is very similar to `top-make.mk', so the large comments
+# NOTE: This file is very similar to 'top-make.mk', so the large comments
 # are not included here. Please see that file for thorough comments on each
 # step.
 #
-# Copyright (C) 2019-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2022 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
@@ -24,7 +24,7 @@
 
 
 # Load the local configuration (created after running
-# `./project configure').
+# './project configure').
 include reproduce/software/config/LOCAL.conf
 
 
@@ -34,7 +34,7 @@ include reproduce/software/config/LOCAL.conf
 # Ultimate target of this project
 # -------------------------------
 #
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
 ifeq (x$(maneage_group_name),x$(GROUP-NAME))
 all: $(BDIR)/software/preparation-done.mk
 	@echo "Project preparation is complete.";
@@ -57,12 +57,12 @@ endif
 # Define source Makefiles
 # -----------------------
 #
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
 #
-# To ensure that `prepare' and `make' have the same basic definitions and
-# environment and that all `downloads' are managed in one place, both
-# `./project prepare' and `./project make' will first read `initialize.mk'
-# and `downloads.mk'.
+# To ensure that 'prepare' and 'make' have the same basic definitions and
+# environment and that all 'downloads' are managed in one place, both
+# './project prepare' and './project make' will first read 'initialize.mk'
+# and 'downloads.mk'.
 makesrc = initialize \
           download \
           prepare
@@ -74,7 +74,7 @@ makesrc = initialize \
 # Include all analysis Makefiles
 # ------------------------------
 #
-# See `top-make.mk' for complete explanation.
+# See 'top-make.mk' for complete explanation.
 project-phase = prepare
 include reproduce/analysis/config/*.conf
 include $(foreach s,$(makesrc), reproduce/analysis/make/$(s).mk)
diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk
index 6503172..ac91089 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) 2020-2021 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2022 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
@@ -94,7 +94,7 @@ verify-txt-no-comments-no-space = \
 # (generated in various stages of the analysis.
 #
 # Since each analysis step's data files are already prerequisites of their
-# respective TeX macro file, its enough for `verify.tex' to depend on the
+# respective TeX macro file, its enough for 'verify.tex' to depend on the
 # final TeX macro.
 #
 # USEFUL TIP: during the early phases of your research (when you are
@@ -103,41 +103,41 @@ verify-txt-no-comments-no-space = \
 #
 # Here is a description of the variables defined here.
 #
-#   verify-dep: The major step dependencies of `verify.tex', this includes
+#   verify-dep: The major step dependencies of 'verify.tex', this includes
 #               all the steps that must be finished before it.
 #
 #   verify-changes: The files whose contents are important. This is
-#               essentially the same as `verify-dep', but it has removed
-#               the `initialize' step (which is information about the
+#               essentially the same as 'verify-dep', but it has removed
+#               the 'initialize' step (which is information about the
 #               pipeline, not the results).
 verify-dep = $(subst verify,,$(subst paper,,$(makesrc)))
 verify-check = $(subst initialize,,$(verify-dep))
 $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
 
-        # Make sure that verification is actually requested, the '@' at the
-        # start of the recipe is added so Make doesn't print the commands
-        # on the standard output because this recipe is run on every call
-        # to the project and can be annoying (get mixed in the middle of
-        # the analysis outputs or the LaTeX outputs).
+#	Make sure that verification is actually requested, the '@' at the
+#	start of the recipe is added so Make doesn't print the commands on
+#	the standard output because this recipe is run on every call to the
+#	project and can be annoying (get mixed in the middle of the
+#	analysis outputs or the LaTeX outputs).
 	@if [ x"$(verify-outputs)" = xyes ]; then
 
-          # Make sure the temporary output doesn't exist (because we want
-          # to append to it). We are making a temporary output target so if
-          # there is a crash in the middle, Make will not continue. If we
-          # write in the final target progressively, the file will exist,
-          # and its date will be more recent than all prerequisites, so
-          # next time the project is run, Make will continue and ignore the
-          # rest of the checks.
+#	  Make sure the temporary output doesn't exist (because we want to
+#	  append to it). We are making a temporary output target so if
+#	  there is a crash in the middle, Make will not continue. If we
+#	  write in the final target progressively, the file will exist, and
+#	  its date will be more recent than all prerequisites, so next time
+#	  the project is run, Make will continue and ignore the rest of the
+#	  checks.
 	  rm -f $@.tmp
 
-          # Verify the figure datasets.
+#	  Verify the figure datasets.
 	  $(call verify-txt-no-comments-leading-space, \
 	         $(a2mk20f1c), 76fc5b13495c4d8e8e6f8d440304cf69)
 
-          # Verify TeX macros (the values that go into the PDF text).
+#	  Verify TeX macros (the values that go into the PDF text).
 	  for m in $(verify-check); do
 	    file=$(mtexdir)/$$m.tex
-	    if   [ $$m == download  ]; then s=64da83ee3bfaa236849927cdc001f5d3
+	    if   [ $$m == download  ]; then s=5d0ab54ca95366d1aab12196966dd3b6
 	    elif [ $$m == format    ]; then s=e04d95a539b5540c940bf48994d8d45f
 	    elif [ $$m == demo-plot ]; then s=48bffe6cf8db790c63a33302d20db77f
 	    else echo; echo "'$$m' not recognized."; exit 1
@@ -145,7 +145,7 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex)
 	    $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp)
 	  done
 
-          # Move temporary file to final target.
+#	  Move temporary file to final target.
 	  mv $@.tmp $@
 	else
 	  echo "% Verification was DISABLED!" > $@