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'.

13 files changed, 39 insertions, 23 deletions

diff --git a/reproduce/analysis/bash/download-multi-try b/reproduce/analysis/bash/download-multi-try.sh
index d7e9be2..bea88d5 100755
--- a/reproduce/analysis/bash/download-multi-try
+++ b/reproduce/analysis/bash/download-multi-try.sh
@@ -1,14 +1,19 @@
-#!/bin/sh
+#!/usr/bin/env sh
 #
 # Attempt downloading multiple times before crashing whole project. From
 # the top project directory (for the shebang above), this script must be
 # run like this:
 #
-#   $ /path/to/download-multi-try downloader lockfile input-url downloaded-name
+#   $ $SHELL /path/to/download-multi-try.sh downloader lockfile \
+#                                           input-url downloaded-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.
+# NOTE:
+# - This script doesn't have a Shebang because in different stages it
+#   should be built with different shells ('/bin/sh' before Maneage
+#   installs its own shell and afterwards with Maneage's own shell).
+# - 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.
 #
 # Due to temporary network problems, a download may fail suddenly, but
 # succeed in a second try a few seconds later. Without this script that
@@ -26,7 +31,7 @@
 # reason, you don't want to use a lock file, set the 'lockfile' name to
 # 'nolock'.
 #
-# Copyright (C) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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 1090e44..5860806 100644
--- a/reproduce/analysis/config/INPUTS.conf
+++ b/reproduce/analysis/config/INPUTS.conf
@@ -70,9 +70,10 @@
 #                   file). Don't use this if you give the 'fitsdatasum'
 #                   keyvalue.
 #
-#   INPUT-%-fitsdatasum: The FITS standard DATASUM value for HDU number 1
-#                        of the FITS file (counting from 0). Don't use this
-#                        if you give the 'sha256' keyword.
+#   INPUT-%-fitsdatasum: The FITS standard DATASUM value for the HDU given
+#                        to '-fitshdu' (below) of the FITS file (counting
+#                        from 0). Don't use this if you give the 'sha256'
+#                        keyword.
 #
 #   INPUT-%-fitshdu: The HDU identifier (counter from 0, or name) to use
 #                    for the verification. This is only relevant in the
@@ -104,7 +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) 2018-2023 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/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf
index c2fa79c..ba8c960 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) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf
index 7bafc4b..1ab7de1 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) 2020-2023 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/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf
index 2aa2e9a..7821306 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) 2018-2023 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/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf
index db7751d..031085d 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) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk
index 325280d..a20abc6 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) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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 9e8db4a..92e5eff 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -1,6 +1,6 @@
 # Project initialization.
 #
-# Copyright (C) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -469,7 +469,7 @@ dist-software:
 # 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
+downloadwrapper = $(bashdir)/download-multi-try.sh
 inputdatasets := $(foreach i, \
                    $(patsubst INPUT-%-sha256,%, \
                      $(filter INPUT-%-sha256,$(.VARIABLES))) \
@@ -672,7 +672,7 @@ print-general-metadata = \
 # 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.
-$(mtexdir)/initialize.tex: | $(mtexdir)
+$(mtexdir)/initialize.tex:
 
 #	Version and title of project. About the starting '@': since these
 #	commands are run every time with './project make', it is annoying
diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk
index 791108b..66c6859 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) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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
@@ -128,6 +128,11 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \
 #	  use PGFPlots, then you should remove the '-shell-escape' option
 #	  for better security. See https://savannah.nongnu.org/task/?15694
 #	  for details.
+#
+#	  We need the modification to 'LD_LIBRARY_PATH' because we do not
+#	  build LaTeX from source and it uses '/bin/sh' (among other
+#	  possible system-wide things).
+	  export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$p"/paper.tex
 	  biber paper
 
@@ -158,6 +163,11 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl
 
 #	  See above for a warning and brief discussion on the the pdflatex
 #	  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):$$LD_LIBRARY_PATH"
 	  pdflatex -shell-escape -halt-on-error "$$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 36f5294..2cc1187 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) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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 460433b..2689e64 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) 2018-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2018-2025 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 930c2a9..7d92d72 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) 2019-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2019-2025 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 aa026b5..c74f8ca 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) 2020-2023 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+# Copyright (C) 2020-2025 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