Configuration: no dependency on /bin/sh and useful run-time options

SUMMARY: no change necessary in your project, this commit only involves
changes in how already-existing software are built. Some handy options have
also been added to the top-level project script and the copyright years
have been updated.

Until now, if the host's '/bin/sh' had conflicts with the Maneage
environment, the configuration of Maneage would crash as soon as we entered
the building of high-level software. The full scenario is described in the
comments of the newly added 'reproduce/software/shell/prep-source.sh'. This
is most relevant when building older Maneage'd project in newer
environments.

With this commit, the following changes were made to avoid the problem
above:

  - Maneage edits the source code of all installed software to replace
    '/bin/sh' with Maneage's own shell before the programs are
    built. Through this, we were able to solve the problem described
    above.

  - The portable '#!/usr/bin/env sh' shebangs are now used at the start of
    the scripts that run during configure time so it uses the first
    available shell that it finds in its PATH (the system's before Dash is
    built), then Dash, and after Dash is built, Bash.

  - For TeXLive, since we don't install it from source, it was necessary to
    add the libraries necessary for the local '/bin/sh' in LD_LIBRARY_PATH.

Some high-level options have been added to the './project' script to
simplify certain operations:

  --keep-going: do not stop upon the first crash, but keep going on to
    build targets until all build-able targets have been built. This is
    very useful for debugging large pipelines and allows you to isolate the
    problematic part of your project.

  --highlight-all: equivalent to calling both '--highlight-new' &
    '--highlight-notes'.

10 files changed, 63 insertions, 30 deletions

diff --git a/reproduce/software/config/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in
index 5ee1ff7..341a78e 100644
--- a/reproduce/software/config/LOCAL.conf.in
+++ b/reproduce/software/config/LOCAL.conf.in
@@ -3,7 +3,7 @@
 # This is just a template for the './project configure' script to fill
 # in. Please don't make any change to this file.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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/software/config/TARGETS.conf b/reproduce/software/config/TARGETS.conf
index 3d35eed..a8b396e 100644
--- a/reproduce/software/config/TARGETS.conf
+++ b/reproduce/software/config/TARGETS.conf
@@ -1,7 +1,7 @@
 # Necessary high-level software to build in this project.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # 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/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index e34d9b8..1a81ef1 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -1,8 +1,8 @@
 # sha512 checksums of all the necessary software tarballs.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # 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/software/config/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg
index 5ad5112..c3cea11 100644
--- a/reproduce/software/config/numpy-scipy.cfg
+++ b/reproduce/software/config/numpy-scipy.cfg
@@ -7,8 +7,8 @@
 # appropriate sections. Not all packages will use all sections so you
 # should leave out sections that your package does not use.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # 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/software/config/servers-backup.conf b/reproduce/software/config/servers-backup.conf
index 67eff44..d4aa25e 100644
--- a/reproduce/software/config/servers-backup.conf
+++ b/reproduce/software/config/servers-backup.conf
@@ -3,7 +3,7 @@
 # is irrelevant). Note that this is not a to be read as a variable but will
 # be parsed as a list.
 #
-# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 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/software/config/software_acknowledge_context.sh b/reproduce/software/config/software_acknowledge_context.sh
index 043d9aa..deae01b 100755
--- a/reproduce/software/config/software_acknowledge_context.sh
+++ b/reproduce/software/config/software_acknowledge_context.sh
@@ -10,8 +10,8 @@
 # your project to make a smoothly readable English text. Afterwards, please
 # feel free to modify them as you wish.
 #
-# Copyright (C) 2021-2023 Boud Roukema <boud@cosmo.torun.pl>
-# Copyright (C) 2021-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2021-2025 Boud Roukema <boud@cosmo.torun.pl>
+# Copyright (C) 2021-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
 #
 # This script is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by the
diff --git a/reproduce/software/config/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf
index 250a4e6..bb38d5a 100644
--- a/reproduce/software/config/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
@@ -4,23 +4,56 @@
 # name to this variable (you can check in 'ctan.org' to find the official
 # name).
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
 # this notice are preserved.  This file is offered as-is, without any
 # warranty.
 
-
-# Note on 'tex' and 'fancyhdr': These two packages are installed along with
-# the basic installation scheme that we used to install tlmgr, they will be
-# ignored in the 'tlmgr install' command, but will be used later when we
-# want their versions.
+# Notes
+# -----
+#
+# - tex and fancyhdr: These two packages are installed along with the basic
+#   installation scheme that we used to install tlmgr, they will be ignored
+#   in the 'tlmgr install' command, but will be used later when we want
+#   their versions.
 #
-# fancyvrb: Needed by R.
-texlive-packages = tex fancyhdr ec newtx fontaxes xkeyval etoolbox xstring \
-                   xcolor setspace caption footmisc datetime fmtcount \
-                   titlesec preprint ulem biblatex biber logreq pgf pgfplots \
-                   fp courier tex-gyre txfonts times csquotes kastrup \
-                   trimspaces pdftexcmds pdfescape letltxmacro bitset \
-                   mweights fancyvrb
+# - fancyvrb: needed by R.
+texlive-packages = biber \
+                   biblatex \
+                   bitset \
+                   caption \
+                   courier \
+                   csquotes \
+                   datetime \
+                   ec \
+                   etoolbox \
+                   fancyhdr \
+                   fancyvrb \
+                   fmtcount \
+                   fontaxes \
+                   footmisc \
+                   fp \
+                   kastrup \
+                   letltxmacro \
+                   logreq \
+                   mweights \
+                   newtx \
+                   pdfescape \
+                   pdftexcmds \
+                   pgf \
+                   pgfplots \
+                   preprint \
+                   setspace \
+                   tex \
+                   tex-gyre \
+                   times \
+                   titlesec \
+                   trimspaces \
+                   txfonts \
+                   ulem \
+                   xcolor \
+                   xkeyval \
+                   xpatch \
+                   xstring
diff --git a/reproduce/software/config/texlive.conf b/reproduce/software/config/texlive.conf
index 71878e5..0babd69 100644
--- a/reproduce/software/config/texlive.conf
+++ b/reproduce/software/config/texlive.conf
@@ -2,7 +2,7 @@
 #
 # installdir: Install directory
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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/software/config/urls.conf b/reproduce/software/config/urls.conf
index 3a86d2d..a5998d5 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -3,8 +3,8 @@
 # If un-commented the URLs of this file will be used. Otherwise default
 # servers (primarily on 'zenodo.org') will be checked for the tarball.
 #
-# Copyright (C) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2020-2023 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 Raul Infante-Sainz <infantesainz@gmail.com>
 #
 # 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/software/config/versions.conf b/reproduce/software/config/versions.conf
index afb0535..e8b8542 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -1,8 +1,8 @@
 # Versions of the various dependencies
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
-# Copyright (C) 2019-2023 Raul Infante-Sainz <infantesainz@gmail.com>
-# Copyright (C) 2022-2023 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
+# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 Raul Infante-Sainz <infantesainz@gmail.com>
+# Copyright (C) 2022-2025 Pedram Ashofteh Ardakani <pedramardakani@pm.me>
 #
 # Copying and distribution of this file, with or without modification, are
 # permitted in any medium without royalty provided the copyright notice and