Configuration: fixed portability issues, add jq and updated GCCHEADmaneage

Summary: this commit will not affect your analysis: only the version of GCC
has been updated for portability and jq (a JSON parser) has been added.

Until now, several portability issues existed in Maneage, causing problems
mostl on macOS, but some also some on GNU/Linux. They are listed below
along with the fix.

With this commit, the problems mentioned above have been fixed:

 - 'pkg-config' on macOS needed some manual steps for a successful
   installation. The cause was its improper checks on the macOS "carbon"
   library. So we now manually fix this check within the code to fix the
   problem. This was found and fixed by Martin Wiesmann.

 - Apple chip variants like M1 Pro, M1 Max, M1 Ultra, M2 Pro, etc could not
   be properly recognized as a macOS system since we expected a single
   word. This was solved by using pattern matching instead. Found and fixed
   by Martin Wiesmann.

 - macOS's sha512sum wraps the 128-character hex hash across two output
   lines (80 + 48 chars) and the command that we used to read the output
   would only captured the first 80 characters, so checksums never
   matched. The solution was to merge the lines before the check. Found and
   fixed by Martin Wiesmann.

 - When a checksum failed, the script exited with an error but left the bad
   '.unchecked' file on disk. On the next run, the download script saw the
   file already existed and skipped downloading entirely. As a result, the
   corrupt file was passed to the checksum check again, failing
   forever. The fix was to remove the file when we confirmed a bad
   download. Found and fixed by Martin Wiesmann.

 - When the server of a file returns a HTML output instead of the file we
   want, the download script could not detect and would assume that the
   download was successful. Therefore, it would always crash with a
   checksum error. The fix was to check the first few bytes of the output
   and consider it failed if we detect '<html' in them. Found and fixed by
   Martin Wiesmann.

 - Unzip could not be built due to linking to old C library constructs. The
   fix was to edit that part of the code before starting the build. Found
   and fixed by Faezeh Bidjarchian.

 - top-prepare.mk: in a few cases, we had incorrectly written './project
   prepare' (which does not exist!); by Mohammad Akhlaghi.

 - Tar's 'acl' features were causing crashes with GCC 16.1.1 on an Arch
   GNU/Linux. Since this feature is not relevant in Maneage, the fix was to
   disable it; by Mohammad Akhlaghi.

 - To disable CFITSIO's fortran library (which could be problematic in
   macOS), we were using the wrong command! Found and fixed by Martin
   Wiesmann.

 - GCC 15.2.0 (the previous version on the 'maneage' branch) needed more
   patches to build with deprecated Linux headers (that are no longer
   present in Arch GNU/Linux, and will be removed from other distros in due
   time). The fix was to upgrade GCC to the latest version of 16.1.0 by
   Mohammad Akhlaghi.

 - Zenodo is no longer checked at the start of the Maneage
   configuration. This is because from early 2025, Zenodo does not allow
   having so many files in a single project, as described in this task:
   https://savannah.nongnu.org/task/?16621. Therefore many of the new
   software (since then) are no longer on Zenodo. Implemented by Mohammad
   Akhlaghi.

 - initialize.mk: when there was no 'maneage' branch in the project, a
   warning was printed when writing the LaTeX macros. However, this is only
   relevant when compiling the PDF. So when the user hasn't activated the
   PDF creation variable, this warning was not relevant and was just
   annoying. The fix was to put a condition and only print it when it can
   be useful by Mohammad Akhlaghi.

 - README-hacking.md:
   - There was no checklist for maintainers; by Mohammad Akhlaghi
   - Incorrect arXiv URL to Eskandarlou+2026; found by Boud Roukema.

Furthermore, the jq program has been added to Maneage with this commit; it
is useful when it is necessary to parse/edit JSON files.

2 files changed, 103 insertions, 60 deletions

diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 92fa8f0..000f62d 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -369,14 +369,17 @@ $(ibidir)/tar-$(tar-version): \
               $(ibidir)/zlib-$(zlib-version) \
               $(ibidir)/bzip2-$(bzip2-version)
 
-#	About the onfigurations: nls and iconv were creating problems with
-#	the dependencies on MacOs and are not relevant in the context of
-#	Maneage, hence, they are disabled.
+#	About the configurations: disabled because they are not relevant in
+#	the context of Maneage usage.
+#	  - nls: conflicts with iconv on macOS.
+#	  - acl: causing crashes when Tar was compiled with GCC 16.1.1.
 	$(call unsafe-config)
 	tarball=tar-$(tar-version).tar.lz
 	$(call import-source, $(tar-url), $(tar-checksum))
 	$(call gbuild, tar-$(tar-version), , \
-	               --disable-nls am_cv_func_iconv=no, \
+	               --disable-nls \
+	               --disable-acl \
+	               am_cv_func_iconv=no, \
 	               -j$(numthreads) V=1)
 	echo "GNU Tar $(tar-version)" > $@
 
@@ -417,35 +420,56 @@ $(ibidir)/pkg-config-$(pkgconfig-version): $(ibidir)/tar-$(tar-version)
 #	'pkg-config' is built first. But when we don't have a clean build
 #	(and 'libiconv' exists) there will be a problem. So before
 #	re-building 'pkg-config', we'll remove any installation of
-#	'libiconv'.
+#	'libiconv'. This can create a known bug:
+#	https://savannah.nongnu.org/bugs/?67001
 	rm -f $(ildir)/libiconv* $(idir)/include/iconv.h
 
-#	Some Mac OS systems may have a version of the GNU C Compiler (GCC)
-#	installed that doesn't support some necessary features of building
-#	Glib (as part of pkg-config), so we will disable pkg-config's
-#	internal Glib for Mac systems, and to be further safe, we'll make
-#	sure it will use LLVM's Clang.
-#
-#	On macOS systems, to ensure that Clang can build pkg-config, take
-#	the following steps:
-#	1. Install the latest Glib via Homebrew:
-#	    brew install glib
-#	2. Set these environment variables before configuring Maneage:
-#	    export GLIB_CFLAGS=$(pkg-config --cflags glib-2.0)
-#	    export GLIB_LIBS=$(pkg-config --libs glib-2.0)
-#   	3. Ensure PKG_CONFIG_PATH includes Homebrew's pkgconfig:
-#	    export PKG_CONFIG_PATH=/opt/homebrew/lib/pkgconfig:$PKG_CONFIG_PATH
+#	On GNU/Linux no changes necessary, so we'll start with those. If
+#	the runner is on a macOS, some changes are necessary.
+	export compiler=""
+	confsh=./configure
 	if [ x$(on_mac_os) = xyes ]; then
-	  extra_pkgconf=""
+
+#	  On macOS we force Clang, because some GCC versions shipped with
+#	  Xcode lack features needed to build Glib.
 	  export compiler="CC=clang"
-	else
-	  export compiler=""
-	  extra_pkgconf="--with-internal-glib"
+
+#	  The bundled glib's gatomic.c uses integer-to-pointer conversions
+#	  that newer Clang (Xcode 26+) treats as hard errors on all macOS
+#	  architectures.
+	  CFLAGS="-Wno-int-conversion $$CFLAGS"
+
+#	  On macOS ARM64 the bundled glib sub-configure checks for Carbon
+#	  support with the C preprocessor only. Since 'Carbon/Carbon.h'
+#	  exists in the Xcode SDK on Apple Silicon, the check passes and
+#	  '-framework Carbon' is appended to LDFLAGS. But Carbon cannot
+#	  actually be linked on ARM64, so every subsequent linker test in
+#	  glib's configure fails silently and libglib-2.0.la is never
+#	  created. We work around this by passing gbuild a tiny wrapper
+#	  script (instead of ./configure) that patches glib/configure to
+#	  force glib_have_carbon=no before the real configure runs.
+#
+#	  NOTE: the initial two SPACES in the SED command are very
+#	  important (see 'glib/configure'): without them, the wrong
+#	  variable will be set.
+	  confsh=$(ddir)/pkg-config-configure
+	  printf '#!/bin/sh\n' > $$confsh
+	  printf 'sed -i.bak "s/^  glib_have_carbon=yes$$/' >> $$confsh
+	  printf                '  glib_have_carbon=no/"' >> $$confsh
+	  printf                ' glib/configure\n' >> $$confsh
+	  printf 'exec ./configure "$$@"\n' >> $$confsh
+	  chmod +x $$confsh
 	fi
+
+#	Configuration options:
+#	--with-internal-glib: the internal glib is necessary because
+#	       without it, we have many problems in macOS.
 	export CFLAGS="-std=$(std_c_old) $$CFLAGS"
 	$(call gbuild, pkg-config-$(pkgconfig-version), static, \
-		$$compiler $$extra_pkgconf \
-		--with-pc-path=$(ildir)/pkgconfig, V=1)
+	       $$compiler \
+	       --with-internal-glib \
+	       --with-pc-path=$(ildir)/pkgconfig, V=1, , $$confsh)
+	if [ -f $$confsh ]; then rm $$confsh; fi # Only on macOS.
 	echo "pkg-config $(pkgconfig-version)" > $@
 
 
@@ -1458,32 +1482,6 @@ $(ibidir)/gcc-$(gcc-version): $(ibidir)/binutils-$(binutils-version)
 #	  first look into its own 'include' directory before anything else.
 	  export CPPFLAGS="-I$$(pwd)/include $(CPPFLAGS)"
 
-#	  In the GNU C Library 2.36 (which is more recent than GCC 12.1.0),
-#	  the 'linux/mount.h' (loaded by 'linux/fs.h', which is loaded by
-#	  'libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp'
-#	  in GCC) conflicts with 'sys/mount.h' which is directly loaded by
-#	  the same file! This is a known conflict in glibc 2.36 (see
-#	  [1]). As described in [1], one solution is the final job done in
-#	  [2]. We therefore do this process here: 1) Not loading
-#	  'linux/fs.h', and adding the necessary macros directly.
-#
-#	  [1] https://sourceware.org/glibc/wiki/Release/2.36#Usage_of_.3Clinux.2Fmount.h.3E_and_.3Csys.2Fmount.h.3E
-#         [2] https://reviews.llvm.org/D129471
-	  sed -e's|\#include <linux/fs.h>||' \
-	      -e"s|FS_IOC_GETFLAGS;|_IOR('f', 1, long);|" \
-	      -e"s|FS_IOC_GETVERSION;|_IOR('v', 1, long);|" \
-	      -e"s|FS_IOC_SETFLAGS;|_IOW('f', 2, long);|" \
-	      -e"s|FS_IOC_SETVERSION;|_IOW('v', 2, long);|" \
-	      -i libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp
-
-#	  Bug in GCC 15.2.0 using glibc 2.43 (see [1]) as fixed in [2].
-#	  [1] https://patchwork.ozlabs.org/project/gcc/patch/e1679277-d7c9-49aa-8365-a8dca082d9bd@web.de
-#	  [2] https://github.com/johnny-mnemonic/toolchain-autobuilds/commit/9585fdfc
-	  sed -e's|char \*q = strchr (p + 1,|const char \*q = strchr (p + 1,|' \
-	      libgomp/affinity-fmt.c > affinity-fmt-tmp.c
-	  mv affinity-fmt-tmp.c libgomp/affinity-fmt.c
-
-
 #	  Set the build directory for the processing.
 	  mkdir build
 	  cd build
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index d059544..281bd84 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -465,7 +465,7 @@ $(ibidir)/cfitsio-$(cfitsio-version):
 	$(call gbuild, cfitsio-$(cfitsio-version), , \
 	               $$confopts \
 	               --disable-curl \
-	               --disable-fortran \
+	               --without-fortran \
 	               --enable-reentrant \
 	               --with-bzip2=$(idir), , \
 	               make fpack funpack)
@@ -1764,6 +1764,20 @@ $(ibidir)/imfit-$(imfit-version): \
 	rm -rf $$unpackdir
 	echo "Imfit $(imfit-version) \citep{imfit2015}" > $@
 
+# jq (to parse JSON files on the command-line) uses the external Oniguruma
+# regular expression library that has ended development in 2025-04-24, see
+# https://github.com/kkos/oniguruma. If this library ('libonig') is present
+# on the host, jq will build with that: causing a leaking of os environment
+# into the Maneage'd environment. Fortunately, jq maintains a copy of this
+# library in its own source (within its tarball) and will build it with the
+# '--with-oniguruma=builtin' configuration option.
+$(ibidir)/jq-$(jq-version):
+	tarball=jq-$(jq-version).tar.lz
+	$(call import-source, $(jq-url), $(jq-checksum))
+	$(call gbuild, jq-$(jq-version), static, \
+	               --with-oniguruma=builtin, V=1)
+	echo "jq $(jq-version)" > $@
+
 # This is the LIGO lscsoft package 'metaio' [1] (to be distinguished from
 # some other packages with the same name).
 #
@@ -1771,7 +1785,7 @@ $(ibidir)/imfit-$(imfit-version): \
 $(ibidir)/metaio-$(metaio-version):
 	tarball=metaio-$(metaio-version).tar.lz
 	$(call import-source, $(metaio-url), $(metaio-checksum))
-	$(call gbuild, metaio-$(metaio-version), static)
+	$(call gbuild, metaio-$(metaio-version), static,, V=1)
 	echo "Lscsoft Metaio $(metaio-version)" > $@
 
 # Minizip 1.x is actually distributed within zlib. It doesn't have its own
@@ -2279,14 +2293,45 @@ $(ibidir)/vim-$(vim-version):
 	rm -rf $$unpackdir
 	echo "VIM $(vim-version)" > $@
 
-$(ibidir)/unzip-$(unzip-version): $(ibidir)/gzip-$(gzip-version)
+$(ibidir)/unzip-$(unzip-version):
+
+#	Prepare the tarball and build directory.
 	tarball=unzip-$(unzip-version).tar.lz
 	$(call import-source, $(unzip-url), $(unzip-checksum))
-	$(call gbuild, unzip-$(unzip-version), static,, \
-	               -f unix/Makefile generic \
-	               CFLAGS="-DBIG_MEM -DMMAP",,pwd, \
-	               -f unix/Makefile generic \
-	               BINDIR=$(ibdir) MANDIR=$(idir)/man/man1 )
+
+#	Unpack and go into the directory.
+	export LDFLAGS="$$LDFLAGS -static"
+	cd $(ddir)
+	rm -fr unzip-$(unzip-version)/
+	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
+	cd unzip-$(unzip-version)/
+
+#	Remove reference to the old 'gmtime' function and include the
+#	system's 'time.h instead.
+	sed -i -e's|struct tm *gmtime(), *localtime();|#include <time.h>|' \
+	       -e'/gmtime/d; /localtime/d' unix/unxcfg.h
+
+#	The 'NO_DIR' variable causes conflicts: the unzip code has its own
+#	internal fallback implementation called 'NO_DIR'. The modern Linux
+#	system already provides a standard implementation using
+#	'dirent.h'. These two systems conflict with each other. This causes
+#	compilation errors such as conflicting types for DIR and invalid
+#	use of DIR.
+	sed -i -e's/-DNO_DIR//g' unix/configure
+	sed -i -e's/#ifdef NO_DIR/#if 0/g' unix/unix.c
+	sed -i -e's/-DNO_DIR//g' -e's/-U_NO_DIR//g' unix/Makefile
+
+#	Since unzip is no longer maintained, it uses an old C standard.
+	export CFLAGS="-std=gnu89 -fcommon"
+
+#	Build and install
+	make SHELL=$(ibdir)/bash -f unix/Makefile generic
+	make SHELL=$(ibdir)/bash install -f unix/Makefile \
+	     generic BINDIR=$(ibdir) MANDIR=$(idir)/man/man1
+
+#	Go back to the top build directory, clean up and finalize.
+	cd $(ddir)
+	rm -rf unzip-$(unzip-version)/
 	echo "Unzip $(unzip-version)" > $@
 
 $(ibidir)/zip-$(zip-version):