IMPORTANT: software configuration optimized and better modularized

Summary: after merging this commit into your project, it should be
re-configured since the location of software installation files like
'LOCAL.conf' or the LaTeX macros of the software environment have
changed. But it should not affect the analysis phase of your project.

Until this commit, it was not possible to run a pre-built Maneage'd project
(in a container) on a newly cloned Maneage'd project source. This was
because the containers should be read-only, but during the various checks
of the configuration (to verify that we are using the same software
environment in the container and the source), we were writing/testing many
things in the build directory, and 'LOCAL.conf' which was actually in the
source directory!

Furthermore, the '.local' and '.build' were built at configure time, making
it hard to run the same container from a newly cloned Maneage'd project. To
make things harder for the scenario above, the 'configure.sh' script would
pause on every message and didn't have a quiet mode (making it practically
impossible to run './project configure' before './project make' on every
container run).

With this commit, all these issues have been addressed and it is now
possible to simply get a built container, clone a Maneage'd project and run
the analysis (using the built environment of the container that is verified
on every run). The respective changes/additions are described below:

 - The high-level container scripts ('apptainer.sh' and 'docker.sh', along
   with their READMEs) have been moved to the 'reproduce/software/shell'
   directory and the old 'reproduce/software/containers' directory has been
   deleted. This is because we have classified the software files by their
   language/format and the container scripts are scripts in the end.

 - The './project' script:

    - Now has two extra options: '--quiet' and '--no-pause'. Both are
      directly passed to the 'configure.sh' script. They will respectively
      disable any informative printed message or any pause after that
      message (if it is printed).

    - The '--build-dir' option is now also relevant for './project make':
      when it is given, it will re-create the two '.build' and '.local'
      symbolic links at the top source directory in all scenarios
      ('configure', 'make' or 'shell'). This will allow both the
      configuration, analysis and shell phases to safely assume they exist
      and match the user's desire at run-time.

    - The build/analysis directory's sub-directories that need to be built
      before 'top-make.mk' are now built in a separate function to help in
      readability.

 - The 'configure.sh' script:

    - For developers: a new 'check_elapsed' variable has been defined that
      will enable the newly added 'elapsed_time_from_prev_step'
      function. This function should be used from now on at the end of
      every major step to help find bottlenecks.

 - The targets of the software in 'pre-make-build.sh' now also have the
   version of the software in their file name. Until now, they didn't have
   the version, so there was no way to detect if the software has been
   updated or not in the source. For Lzip and Make (that also get built
   after GCC), the ones in this script have a '-pre-make' suffix also.

 - 'Local.conf.in' now has descriptions for every variable.

 - The '-std=gnu17' option is now used instead of '-std=c17' for basic
   software that cannot be built without specifying the C standard in GCC
   15.1 (described in previous commit: 2881fc0a6205). See [1] for more
   details; in summary: '-std=gnu17' is also supported on macOS's Clang and
   has some features that 'pkg-config' needs

 - Generally: some longer code lines have been broken or indentation
   decreased to fit the 75 character line length. This has not reduced
   readability however. For example the long 'echo' commands are now
   replaced by multiple 'printf's, or the indentation is still clearly
   visible.

The seeds of the work on this commit started by a branch containing three
commits by Giacomo Lorenzetti (133 insertions, 100 deletions). Upon merging
with the main 'maneage' branch, they were generalized and re-organized to
become this commit.

The following issues have also been addressed with this commit:

 - The LaTeX calls (during the building of 'paper.pdf') do not contain
   Maneage'd dynamic libraries. This is because we don't build the LaTeX
   binaries from source, an TeXLive manager uses the host environment.

 - The 'docker.sh' script:

    - Adds the '--project-name' option: its internal variable existed, but
      the option for the user to define it at run-time was not.

    - Ported to macOS: it does not check being a member of the 'docker'
      group, and finds the number of threads using macOS-specific tools.

 - The 'apptainer.sh' script:

    - Now installs 'wget' in the base container also (necessary when the
      user doesn't have the tarballs).

[1] https://savannah.nongnu.org/bugs/?67068#comment2

1 files changed, 71 insertions, 0 deletions

diff --git a/reproduce/software/shell/apptainer-README.md b/reproduce/software/shell/apptainer-README.md
new file mode 100644
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+++ b/reproduce/software/shell/apptainer-README.md
@@ -0,0 +1,71 @@
+# Maneage'd projects in Apptainer
+
+Copyright (C) 2025-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org>\
+Copyright (C) 2025-2025 Giacomo Lorenzetti <glorenzetti@cefca.es>\
+See the end of the file for license conditions.
+
+For an introduction on containers, see the "Building in containers" section
+of the `README.md` file within the top-level directory of this
+project. Here, we focus on Apptainer with a simple checklist on how to use
+the `apptainer-run.sh` script that we have already prepared in this
+directory for easy usage in a Maneage'd project.
+
+
+
+
+
+## Building your Maneage'd project in Apptainer
+
+Through the steps below, you will create an Apptainer image that will only
+contain the software environment and keep the project source and built
+analysis files (data and PDF) on your host operating system. This enables
+you to keep the size of the image to a minimum (only containing the built
+software environment) to easily move it from one computer to another.
+
+ 1. Using your favorite text editor, create a `run.sh` in your top Maneage
+    directory (as described in the comments at the start of the
+    `apptainer.sh` script in this directory). Just add `--build-only` on
+    the first run so it doesn't go onto doing the analysis and just sets up
+    the software environment. Set the respective directory(s) based on your
+    filesystem (the software directory is optional). The `run.sh` file name
+    is already in `.gitignore` (because it contains local directories), so
+    Git will ignore it and it won't be committed by mistake.
+
+ 2. Make the script executable with `chmod +x ./run.sh`, and run it with
+    `./run.sh`.
+
+ 3. Once the build finishes, the build directory (on your host) will
+    contain two Singularity Image Format (SIF) files listed below. You can
+    move them to any other (more permanent) positions in your filesystem or
+    to other computers as needed.
+    * `maneage-base.sif`: image containing the base operating system that
+      was used to build your project. You can safely delete this unless you
+      need to keep it for future builds without internet (you can give it
+      to the `--base-name` option of this script). If you want a different
+      name for this, put the same option in your
+    * `maneaged.sif`: image with the full software environment of your
+      project. This file is necessary for future runs of your project
+      within the container.
+
+ 3. To execute your project remote the `--build-only` and use `./run.sh` to
+    execute it. If you want to enter your Maneage'd project shell, add the
+    `--project-shell` option to the call inside `./run.sh`.
+
+
+
+
+
+## Copyright information
+
+This file is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free
+Software Foundation, either version 3 of the License, or (at your option)
+any later version.
+
+This file is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
+more details.
+
+You should have received a copy of the GNU General Public License along
+with this file.  If not, see <https://www.gnu.org/licenses/>.