Until this commit, when we wanted to build the project's PDF within the
tarball (outside of Maneage) and it was necessary to update
'references.tex', the update would not be applied in the PDF. This was
because BibTeX only allows a single '.bib' file that was hard-coded in the
distribution tarball.

With this commit, the temporary Makefile that is also built in the
distribution tarball also creates 'references.bib' when necessary. Thus
fixing the issue above.

Until now, the rule to build the contents of 'make dist' assumed the
default BibLaTeX peculiarities of the main Maneage branch. However, A&A
doesn't use that format and it was problematic for people submitting to
that journal.

With this commit, the necessary corrections have been made to the rule.

Until this commit, some remaining temporary modifications (in
'reproduce/software/make/high-level.mk') had remained! These were made
temporarily to allow a fast build on my local system, but I forgot to
remove them before pushing.

With this commit, they have been revered to the same version on the Maneage
branch (since they are unrelated to the A&A journal modifications).

Until this commit, the LaTeX style and settings of the core Maneage branch
were very generic and customizing for each separate journal required some
time to prepare the LaTeX style.

With this commit, a first attempt at customization of Maneage for the LaTeX
styles of the A&A journal. Note that EDP Science (the publisher of A&A) has
only claimed copyright in their style files, but hasn't actually specified
a license. Given that they have no objection to arXiv or Overleaf freely
distributing their style files, there is no problem is releasing these
files within this branch of Maneage also (only for people who want to use
their style to publish in their journal).

Summary: will not affect existing configuration or analysis.

Until now, the 'clean' rule of 'initialize.mk' paid careful attention to
not remove certain files that were created by the project configuration
phase in the analysis directory. However, in the last few commits, we have
fully decoupled the file creation between the analysis and configure phases
of Maneage. Therefore that extra complexity is no longer necessary also.

With this commit, when './project make clean' is given, besides the
possible LaTeX generated files in the top source directory, we simply
delete the full 'build/analysis/' directory.

Summary: will not affect existing configuration or analysis.

Until this commit, if the user gave the build directory interactively (had
not run './project configure' with '--build-dir'), the '.build' and
'.local' symbolic links were not created, resulting in a crash shortly
afterwards (when Maneage tried to write 'LOCAL.conf' in the build
directory!).

With this commit, the problem is solved by creating these links also when
the build directory is given interactively and after all the sanity checks
have passed.

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

Summary: this will not affect already built/configured projects, only
improving the portability of future builds.

Until this commit, no specific C standard version was given during the
build of Basic software (which use the host's c compiler, culminating in
the building of GCC within Maneage). On the other hand, GCC 15.1 was
recentely released and made available on some operating systems. GCC 15.1
has made C23 its standard C version (from C17), as a result, some of the
basic software crashed and didn't allow Maneage to built on those operating
systems.

With this commit, the '-std=c17' flag has been added to software that
crashed when the host GCC was 15.1. Also, they have been grouped with a
description of this problem in 'versions.conf' so we check the need for
this option in future version updates.

In parallel, some minor edits/clarifications were made in the two
'README-apptainer.md' and 'README-docker.md' files to be more useful.

Summary: it is necessary to re-configure your project (just running
'./project configure -e', not deleting 'build/software' to re-build
software) after this commit, see "Affected files" item below).

Until now, we only had a relatively long set of manual instructions for
building Maneage within Docker in the top-level README. This was hard to
automate, focing Maneage users to write custom commands based on the
instructions and maintain those scripts outside of Maneage. As a result,
experience could not be shared between projects (or at most in the README
file!).

With this commit, a new 'reproduce/software/containers' directory has been
created within Maneage that contains two scripts (with a unified interface)
greatly simplifying the building of the project's software environment
within a container (one script for Apptainer and one for Docker). Two
READMEs have been added for each container to help in their first time
usage. Also, the old checklist within the main README has been replaced
with a short introduction on containers and points the interested readers
to the custom README of each container technology.

Since we wanted the containers to be read-only after build, we needed to
fully decouple the 'build/software' and 'build/analysis', such that
'./project configure' only writes to the former and './project make' only
writes the latter. The file and directories mentioned in the affected files
are cases that both project phases was writing to the 'build/software' and
'build/analysis' directories.

Affected files: 'preparation-done.mk' and 'lockdir' which were previously
in the 'build/software' directory are now made during the 'make' phase and
the 'configure' phase no longer builds the 'build/analysis' or anything
within it. Also, the software version LaTeX macros (which were previously
written during the 'configure' phase in the 'analysis' directory) are now
written in the software directory and copied into the analysis for usage in
LaTeX while building the paper.

Other minor additions in this commit:

  - The './project' script has a new '--timing' option to write the
    starting and ending times of the project in a file. It also builds the
    high-level analysis directories when './project make' is called (but
    before calling 'top-make.mk'.

  - The 'tar' calls in the custom build commands of the software building
    Makefiles now have the '--no-same-owner --no-same-permissions' options
    like the 'tar' call within the 'uncompress' function of
    'build-rules.mk'.

This commit was originally written by Giacomo Lorenzetti only for Apptainer
on the registered commit date. It was later re-implemented from scratch by
Mohammad Akhlaghi to have a unified interface for both Apptainer and Docker
and merged into Maneage on 2025-04-23.

Summary: this will not affect any analysis.

Until this commit, the old version of 'setuptools-rust' did not install
with the updated Python version (see [1]).

With this commit, 'setuptools-rust' is upgraded to version 1.10.2 (from
1.1.2) and 'semantic-version' 2.10.0 (needed by 'setuptools-rust') is
added. In addition this commit:
  - removes a duplicate rule for building 'cycler' in 'python.mk'.
  - comments all the un-commented '*-url' variables of 'urls.conf'.

[1] https://savannah.nongnu.org/bugs/?61731