IMPORTANT: version updates and improved portability

Summary: this commit involves a major version update of many basic software
and Gnuastro's major dependencies. So it may affect your configuration and
analysis.

Until now, the most recent software updates weren't properly tested on
MacOS, causing the software configuration step to fail. In particular, the
'prep-source.sh' (that corrects any hard-coded '/bin/sh' within the
unpacked tarballs of all software) as well as some issues in the 'tar',
'util-linux' and 'ghostscript' programs. These portability issues were
found and fixed by Raul Infante-Sainz and Giacomo Lorenzetti.

With this commit, those portability issues have been addressed while
updating the following software. Also see notes below the list.

   High-level software:
     CFITSIO             4.5.0       -->     4.6.3
     Ghostscript         10.04.0     -->     10.06.0
     Gnuastro            0.23        -->     0.24
     Util-linux          2.40.4      -->     2.41.3
     WCSLIB              8.4         -->     8.5

   Basic software:
     cURL                8.11.1      -->     8.17.0
     GNU Bash            5.2.37      -->     5.3.9
     GNU Binutils        2.43.1      -->     2.45.1
     GNU Coreutils       9.6         -->     9.9
     GNU Diffutils       3.10        -->     3.12
     GNU AWK             5.3.1       -->     5.3.2
     GNU GCC             14.2.0      -->     15.2.0
     GNU Gettext         0.23.1      -->     0.26
     GNU Grep            3.11        -->     3.12
     GNU Gzip            1.13        -->     1.14
     GNU Libunistring    1.3         -->     1.4.1
     GNU M4              1.4.19      -->     1.4.20
     GNU MPFR            4.2.1       -->     4.2.2
     GNU Nano            8.3         -->     8.7
     GNU Readline        8.2.13      -->     8.3.3
     Git                 2.48.1      -->     2.52.0
     Less                668         -->     685
     Libxml2             2.13.1      -->     2.15.1
     OpenSSL             3.4.0       -->     3.6.0
     Perl                5.40.1      -->     5.42.0

The latest versions of Bash and M4 were prepared for the new default C
standard of GCC 15.*, so the '-std=gnu17' was removed for them. Also, while
a new version of Dash was available, it would cause an issue when building
in Apptainer, so it has been described in 'versions.conf' to be aware in
the future updates.

Libgit2 has been removed as a dependency of Gnuastro. The reason is fully
described in the comment on top of Gnuastro's build rule in
'high-level.mk'.

10 files changed, 134 insertions, 89 deletions

diff --git a/reproduce/software/config/checksums.conf b/reproduce/software/config/checksums.conf
index 89738ce..7f786c7 100644
--- a/reproduce/software/config/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -15,43 +15,43 @@
 
 # Basic/low-level programs and libraires (installed in any case)
 # --------------------------------------------------------------
-bash-checksum = 52fa7d14e5f05d7b1b5f64ca110388db119fd6b8d4cc25011e0e25848491507e610259091c56f3ca7a7688ee2547f8a98de2005626b35c29558e71f28e29b848
-binutils-checksum = efbc5957bd22804a860261886598778347e82f9cbc0728d21d26748b7296e34328fdc16252868169594a001a301babbcd0964d9c508523736bc79cac2aff8efc
+bash-checksum = b905e107403ceb25ad92f26ab71d6a7f12b1cadbcb27de9f5fefa7da31e96de0be281f8095170ed36e3fc22237dcfc252ff674925e6123638f6a3e11f3c5ecfd
+binutils-checksum = ad7bbebc0c4e537c15d7537027246e2c1c0d355efcd6a369c7ef91c6491ec6a6e9af24c60b7df7508213abeedbd2e53c41549889073ac1f629b0746b78ee894b
 bzip2-checksum = 929cb1b2d0db8a505e2bafe3ce2c893c8f132dd617c0110e86e19f116b570a85de3c8a635483b530456fc8f8b6698c8190d21313e47607f442807b10489ac86e
 certpem-checksum = d1198511bf1f61a624691c182ecdd57ff468030a4af8b0f0ef248a5ce1f42ed883c684fc5aafdd791d5d3aa24504fbfbab11043231594b1c4e21fdb7247e5a33
-coreutils-checksum = 2afaee98b305f000ab1c9e25b5fec6413c3e385c685f2afe94e3676593c09efca39d007cfda2b3b122e68e94204d2ebe7f50b39300899d8720518d6f74bce019
-curl-checksum = f391f696d725ace63271fe614ab3067b8d55d04be3a160c70bbca388de93670e5fb986dd5dd45e1b62c0327b2b1374ab229bdb5c9df746f70823e0721c9f048d
+coreutils-checksum = 1aa2775ef67ed9ddf30e527fd7b813ba83b43e921e1493d44c016bf2750ccb1478ea08a2cd000a619fb22f800f7f84bb03fff5acdcfad7a45d5aef833fdbf041
+curl-checksum = 5b0213eb1d1c2146c591a72ba0d763c40cf707c7fcc43f4807cccec12ddd3cc63127da0f18f96c2450efc8607812519dbccbc924b5b629712fbc7b02b4976aee
 dash-checksum = f21a2ac71606a5ae8dbda5639d111f385cc44c357c580a83e453b33faa32c92fd83f8ca6c5d2cf720343f8ab1cfec247ca499596f78ee19f62d67cd1d7ae0c69
-diffutils-checksum = 52582c860a4ce544f0c1a3e61bd9a1ce5f13e1c677b67d3713982439760e40b60267b222de3ef0a27065652822d9880a206899528d7ff8d60c7e64b64721b3e1
+diffutils-checksum = 9d42c57a5ae4770b6d84b76f324c7c09c62792cac063048793037281972983dd4c409868545f2460c281f761adba6c49fab3fa227ab5231397809474cedbdfc1
 file-checksum = b843b3c25656e8dec52e64eed6f581b29faf36540e0604a803d61c0f0eca830a01a947b81970b0d8a24a1336a37ae5c96bb2ade59daa16c544b1e82fc7db24e8
 findutils-checksum = 826c643e7f5c5d6976a47eabcd9807e51350d09ee8fc7dc931f2d9276f938f65aa0bd97e6213aa979742234784c120e1a6850a52207c327e1c1a465feb374053
 flock-checksum = f711815035e21b46572bf80e730a55822e5abf4cb29749e476ee6cf4d5027e9a7deeacf5f6b8c37f18f17a0cc7a6d98fb0be3936e97b122707f1cb2306d1e1d9
-gawk-checksum = 13cb59a4ef43e5b0d10f13263dcf5ccd72d9344f3ecc512589ed7f6d059baf8a5ae375d38f7654695e29f0694fc33deba3c7c008d61f09e67df57bf81e573f0c
-gcc-checksum = 40f239730fc0165a0ef48f252a886e9cbe7a95ed53fe2c7a16531d7f3d6faabecb2d868cc895a25f7561e7bb90892e3372652953efd8ac35359a6ac2e18a4447
-gettext-checksum = c53f3a09cbb62a3ba8870f1310da336c084bfc83534d7e9c236f7660f503d638654a91301558f1e4880ead2d629dcd92f7c3dd7e0d981d445b74215d836d19ea
-git-checksum = 6e7ac2188cf3204fceeebffc46f34a8180e53a887987a8e1b9d6c90f84073e4b86d45f39488f69432b1cd0962cd8fbd434c07128fc2e430cd2ec20f1a1fc8b61
+gawk-checksum = 9013f5cb4c08aa13029ecf0c6b5e02ac93a3b500683b07ae8d34d698f0451dd5146a0a5aef96a249112834e27b379869d8e541f6a1b99accf701ba6a48f58f33
+gcc-checksum = f7386218e0993e19da1092bf625791cb9ec269667f7bdf378fef359a304aa08e4d79cb7b9f56d5d7028b53b29071005707a1cad0fd1b770884ab02310ed7b028
+gettext-checksum = ec0aaf00e5ccfd5c0c51be2239590cf9f7f9105b072081c8374caa75c08611e4c1ebfd6ac6a487f7b54f57c2d8b493fe6ab4ca8d62592dba4db5715e67855f3d
+git-checksum = e2a3d2cf272554c0e9fa2abc4cf7b1eff17884911859f17567b76f170996802caa01675a42dbf29af7fc283a07e8dc4a11382ffbd2a03d7d62238e8c598f0b56
 gmp-checksum = ad65de00ecb46cf454ed6c40d2a57ce2528f5fa64df1284dfa15036f1e8cf27760a09a4ecdfcc39048faffb71339bba30d99dd365c54173dbc2ba629bee2fad9
-grep-checksum = b1ad850671290120ca0ced6d1744622d99a903c6e638dd231e89a70a2ab48c382100e218697b6fbbbda8c99316679a7c681383a5e954790bbffb9719bd0d6d8e
-gzip-checksum = 19ef6f51ee8274c08aa188ebd26634a40f91c057ff1ad3253719a7fa0c7ac857de5cf289990e0b9fc67d89ca3abb50db6dbaa7664d2c58275c844712834d5e10
+grep-checksum = 4e39935e26a0d742c0e854135940693166ea142673f50dfd589eedc96dded0e8dcad425e6519ee85d59fdf9d418381ba775a7c560cbeebcdf8a1848339243145
+gzip-checksum = 3c61b50f3a9efabf69b4b91410ffd83e0f3a54f1d465a5326e66972e18fe829eaabc77bf47b89340d59f6c5b57fb4c03e293cb7044c57ad7526c8de9bbc80ed7
 isl-checksum = 615827a86e809c9645e090786008f8b37d7efc7fee6501ff81e937a299a5a72e7998a3965457d1380cb04f7e765b600276d87b7b59cae22d82aa65e71294f499
-less-checksum = 3b52347e1b779a52c89cb18da85a0963eed500e1e94cd3952c0693c56fd0eec4e8606eb02053d451ac92ec8c6e196edd1341eac54515ed84483112513f41f210
+less-checksum = f02557d9b85d4144e530ef8f2e95329b7bd2eba1be2513558cd7359cf520e1e6723c4d62b6dd42082084003ac9cb23c3d1d9ad7ca73d58597f7fedf31e9d08fd
 libiconv-checksum = 1f33fcf7f617990812a26e15092dbb2f9e81400cee117eefd40ade813f7ca17c0b9a50a7a9881b4ab0b9c0be8475528204c347d940cbc667a918570e0bde051a
 libtool-checksum = 2aa6d535b4d644393d7ca5c8f174b09923dbdb50d947ba40917aad75c8cecf957fec7a54717bd3670c44130331b1f08fae3694e32c79c8e187c31e909b3d401b
-libunistring-checksum = 6ca6a2dea2c09b6e8e63eb7ff73ab62b2e2f7c412766209c9f6da5b13a109e3a7cb41e67aaee1fb2b46549965b7df13c508000e40594570abe71819dc9cc2eaf
-libxml2-checksum = 7c2c65ae5017be5d695ec5a0e9bf443fe130d33beec97f31bcdbe74c22ac7745ce02524ca603e701035576bdca91c4cb1cbe67ccad5525f9a4566451a8f0c935
+libunistring-checksum = 3e79a3f5a1c13ce9554071ffecafa24a95ba36e2c1087940aa1ba93957ed14290779d1603b401431eda20c3da5f345a0b8842191a3e65f03fb2667e2a1443e30
+libxml2-checksum = aee3946beba88dba0a4ba573704da0c48de3233e5a1717ac6d8e647f3c8b65131c1b4d320604adedd8eff3364af11a3489a2c26b57b8151b59fca60da3f2a1c3
 lzip-checksum = 513b7ecdee1d6f12298cbbb025286c887c5e6588e1268b489735955f822a8e305e7a8d4d06054a77b2f4c40f8d82e9e6d779cd73d4227ca3cdfe4002b9e42a98
-m4-checksum = 7f8845f99e64d6a45859b9d80b03352a5526b3de0311ca4d6dd6850e504d26dfc90cd21d1640b10382f786213f8fdf20183bff424b3c41ea11432315993ab829
+m4-checksum = f24f0a0f71bb5241f8bbf5cb75e260a546ee9206b80478544944053768fae77f322839e78d5524a2bc5cdc06fa921ca88b1d366ed3c67b745cf55df3a30de158
 make-checksum = 154a0247297a7b0131ff63fa8636d651b33aacc8f4a0dad1db176995b20c2039f4fd58eeb2ec27cc0ca7a95c1853199a4ee35a14afc5084995ecc1d694203412
 mpc-checksum = 76e0720e6287d8b7a3eaa09dc5baa5a2b61dde88198c9e1bc9c458a268a44035d11fbab1c8019501a7ee2d5745c7eddfb0bb3c7297110a0fd9e027acb42d0fc3
-mpfr-checksum = c6013b0f573271a3bc41bc3eb28c61f099c6fc5409096a27624b5ec049e6305a1c48275c6f244d0cbe1fe65f649704c7d5f6487ad24308f6b3becc17032fc222
-nano-checksum = e559c09057ff75cd650f02744dff801750a159785234189e48f976bb4ab90142aca2577a283f80d8eecdc4f2b6c0a55bfe6da69e6aaecc5812f32f923075ca9c
+mpfr-checksum = 40066bbbfb394ad4fc2efcbf633542c43fc6e31e3503d0f8f425649c95cfd6aeed78e889852bdfe23f783b5b13766ebdada9c92e6a921d84c6a8703123e9c165
+nano-checksum = baac691afb7e1c956fa0be16a4857cda9513180e5b5b08d55745f5c5f53ada954301e8ab0aa12c46aeed8f984ad3cb77ea3029ec8ede9dcc76d1c84a9e640a58
 ncurses-checksum = c94eccc1b23a9c6ca9b27881674b19802942802cf21084bd80e45e0b9e50a2d99e0e18a1ecd5cf3e686949982ca93132a7fe2f117a7c4307283db5012b11a2d5
-openssl-checksum = c4c44ab8e4a6d39e6aa69b096a831645c33d5675619d31da6e441452f67e487489b33041a34038a0f8ad596506e17ce8695a8f87bae861700481ecf6b9742b76
+openssl-checksum = 7cf3cfa3a190a8944366393942faab0813c8443dce5bdb8bdf11b7cae3627f9a3ed2698c6785ef4688c42df12983c2a9ce932e58f2e3691e752589dbae5ea363
 patchelf-checksum = f74409c00e7e50a88590267fa0c173f71239f1471985792f7bcdab750d202a9a25383c015987608bbcd6ace5b3642645d46dba63199ba54fabbcb51ae7fca8f6
-perl-checksum = d53da403f2232b487f11df4b0b889babf58350715c7430515ba32e2e7d9996308c5d75ee626906a9f3c56872672c9cfe3880e10c7bb084c178c7c76bb2a5346f
+perl-checksum = d5c782948b97b706fe9650f6a9995591d9b90da3a98866d1db4d20025262d5606f4133222be4b96cc06578323db03759910e96012d8931033feaddca0e156e31
 pkgconfig-checksum = c37ab9336ac15a73bf5a23101f3fd8a04810f39b0679634e420e5d7bbd60a80cfc919122694cf83965beb071d2780681efc8d954ce99d77eb235a4dc7497e250
 podlators-checksum = 2e1e8547b0c890101a9fb8d80807b164a0a708820617a6826127930f85115285a0e4d62ddf8ce2401df14c021521a1b3ce0cad0d308e08f7b3d0c49d1b0dd36f
-readline-checksum = ca08305c5a6d5eb6656a7cdff73aab65c1234de62db8da90335e9ea140b1d4f8a867204bdc49ead3acc5e5236358130e73032bd73de5dfe1eee5bb2c76be5cb2
+readline-checksum = 349248d78cfc1deebdaaefc70a044835139cb8775d74bb33ae2a2600d9daef2b169608a8f706fc803a8d95fe9b309da1db0c6d19fa78eaa67430aff5b13feaa2
 sed-checksum = e801dacce45a08671e65897f85be0a37a29d97f61e846ca17ff870d3ab9f5a639dba73457491087ff637df4a81099b864d2496d59acf17a07916b43bfe0ae480
 tar-checksum = f8d0b543dc4a2a57d61d8a183d7a64d611d11f033c64683f022a7f1f956d352d364a959903a2549ab1256c1a068de51052960cf34a70f355b80e237f654bfac7
 texinfo-checksum = 06e7d95d73380c16f064e119bd8717942fb464c1cbc532fb1833d2d5dfc3cbbcab2a9001a1d03721c347f676e1db22c2a0f78d19d22df379d0393527be411ef3
@@ -85,7 +85,7 @@ bison-checksum = 08c3e9bcf9fc01bc8b3a6c5e5f8ecdf628e07d6ce0874341e9df6d7b2925db7
 boost-checksum = df252f6aabd9b1d5421afc478fa288e947a7c5e11f26e54f0a8619c9ac5e16688c20f44106a429ae798b20a4c97cbf800ee0ac9b2aa7febe1bd2755c88802ac1
 cairo-checksum = 5de8528196b450d01da5cd4562dec0dd8c31028b77640b6c611172f7c5ad1dc9a4d30bd4e38259344c3ee42b979e29be702a3190aae5fbf47c82c79ee0c14a8e
 cdsclient-checksum = 24584eedeb84ab4666cbd2ed0b7264c92c63c9cf090595b75b01dd46f848419d6a7e5cff4db3946695f879d0ee2bfbeb527e88c2be85e769b577302d9b2ad2b7
-cfitsio-checksum = fd40e0cec22bf3a35a7c48ad61a6ebad5a54d3230606c7492161c067b7ccd303ed34d149427bf1d3365e7a3082d89b51df46fc8a9c3d3c0b1eef8756374d711e
+cfitsio-checksum = 60e10544bad66812dca3ff04620051c2c99d047952b5fa6280f4ca443affcbe4806b84f4cb439036b9affd42ab82cf723ae7866aabd33629b25e8edaaba63c72
 cmake-checksum = 3904964eeb256ae4443d000a24ebdbfd76c677aec08d006f8665020f1ebf2008c65b6a1cffd6fb5b8a29cdb52420415ed2e0e2ea258db2e9888dc48068fc3941
 eigen-checksum = 39c1944e0daca50bb01e929edc98e2bfc234accb30ca019dcccfc7b02db5cc81035592be219ae93cc3ec16fe0255e7e4d1f29ca2ad3dfee7e63546c47cb2f807
 emacs-checksum = 91313dced8cd74f9e4a996eef42806aad00fb2576fc77b3694bb7b670624b6a1551ff49c2a3326dbeeba916e5732ca5975b5dc40b3b063f6e73a22839009abe9
@@ -94,10 +94,10 @@ fftw-checksum = 28bd2f620399a415181027d30d7ea193aa487c7a277c9943d0051488908fd87e
 flex-checksum = a18e0dcdd21bd51779fd70e5efc2d77fa7b2a56d4d0e929d8abb437f86d7fcfa2cd09b8268185698200866dac8bec4444c5a7cff3140c515eaa49fc77c5aea66
 freetype-checksum = fb2d89421633a56d4276b192106d930c9f29cf2b70c52d9e13ba0c6a2679b6f69c20ab9f14480522992c263b493f198f24593bdeddb5806a4d801ab7604a5926
 gdb-checksum = 4afd6660d2bbc4c48ce726062fb42217bdaa5974774407358b2624036a2ace48ed853746e4d6b83b9a409cd8fefc622b0727c79da8826e28e3d1444fa3a9d148
-ghostscript-checksum = 2d6422d434cbe6612d4e995022322e17d0167d0d92fe1f6fe122da73558a81fa43025458411e38363a0e30a573cbc6cf997ae7aa562501787d0af88bf1b5b387
+ghostscript-checksum = 516f7f3bf8650ff5cf5a913ac1d69c196dbf62de97b77fba75fad7cfbace5c978a4aff7da0ede3590f56d68b240398ee17a1a504bd8e8ee76a4879b0b3b6a8df
 ghostscript-fonts-gnu-checksum = d8de17e5d920bd3803ecdc07aca224fa5b9a26db847ddae0ecc79488dc3e867ab3155a8565f20df7855e5228bc7f36a549b082ba0b8b56c9b948d6cfb655fdc0
 ghostscript-fonts-std-checksum = 40e01f88dd113c3120686c11da1c4cf4ee77c8db315b21cc936c3ccfb42cad4949e207298ec6d78d03327ff05122fcd75ac82d5e7cdc9698d4bbf1f72b19756a
-gnuastro-checksum = d27399993ab65d1864c915fe107efb298c758e1f24e3f300830f8f120768dd3a54daea1d2af5537e9dd3b50a13a51edd237f434bfbb442ab992828b2dab1386a
+gnuastro-checksum = f777f84d03cc106a12373416ec3617e4c598f7642f6ebf881fd59a3068c8b4cd5ba98195c1e154a4a37d3b22828b618e5ac70157c2775d11032b7e061880aa2d
 gperf-checksum = 854cdb24337f14b0d4199cc97c4a1d2ec7f953ad8125a47a932d93f79bdc067e2de231859ac0e842f14b1a8d80c5606fdc2c295a370df5e85ea15023b478805b
 gsl-checksum = 9a46b431eed536182f31e1ecad781ade214ac8bd885ac88bbfd02b6e08482c294775a529e561d358c1f0211d8d20db4ec99b448b9006c3bf7599c076d3fbbcc3
 hdf5-checksum = 58d6d9a1c201efa0863d9c31d189b4d40b1a9b1fb1ab9cb3fdeb4463f508c043e467aa4d44484c2af111d4e2fb775223286da69568774e6edef285208290c67b
@@ -138,9 +138,9 @@ sextractor-checksum = 4035710f9b8a20a0bb1a3913dab2dadd8444c179bf6dee425e0e8bb66a
 swarp-checksum = 810af6ea0a2dfc7b78b0f6aaa486b80c29f517b90c29f5037d05f31f761e96a55c8b5dcc259e1b435b25f45f01dac45ddba61da84000a69676cce119880bb05d
 swig-checksum = ecb1d940f584c23df036a8f77288916003f861851dfdf836ddc5bc45b95312f9259150084191c1d9f086c006e64e12a4db22f7ea382fbb71667b811b8f99995d
 tides-checksum = c3360ff0d023b43749ba09a33302ca059f017a157b3ce7cdcf4f1a1578e90d3e7fa420077043adbee6b1ebf94bd698c8d6b279012f36d2a05b4de5351e30e108
-util-linux-checksum = 9d421976a344f982f2bd910f0c888a7df4370a1e367c7d2582d03a58cb8500f1fe65cf6a7164c492a9ebd76bff04560c344b3a0f63ecdb372bfea2379b383030
+util-linux-checksum = 3053377ca3e399a12ea86ba96ac38749ff15a42e76742ab4346eb2f96c8b24564077db44c5b173e8474c8770846dc355b1281a697ef5a168e239b1b6d693469c
 vim-checksum = 85d083fcf3638f2c3a049b88da46d569d6a250ae132f3821d440c07c4792befffc09e4235241ca96d7b0307a1bb96cd2222ac8a63fb41c6add8c2bdc6c17aabb
-wcslib-checksum = cc72804611df1b0087faed2ec19edbc17352cc631559edc8ceb03792162837cdaa6bbf144897c69a58c9fab7e569a1958149be7eaea6552d72190406e4755d12
+wcslib-checksum = 68f40f268d4a4d6d052e444859070138f90f17fb1723cba2da88293b5f7a372885461a09da1ca0ba1686d08e7d731cae52e305b65a6f5edf13586f48a61dca55
 xlsxio-checksum = 22870fda7bd4eefd5fea2a9ad7530c9049135129d9b69805091777e6b54b2fc6c3f0e69c6954f36bce54eebbfeccaf637cce9e271a593221a4296d6632470a6c
 yaml-checksum = dadd7d8e0d88b5ebab005e5d521d56d541580198aa497370966b98c904586e642a1cd4f3881094eb57624f218d50db77417bbfd0ffdce50340f011e35e8c4c02
 
diff --git a/reproduce/software/config/urls.conf b/reproduce/software/config/urls.conf
index 8bf7b23..4a19fba 100644
--- a/reproduce/software/config/urls.conf
+++ b/reproduce/software/config/urls.conf
@@ -25,7 +25,7 @@
 #curl-url = https://curl.haxx.se/download
 #dash-url = http://gondor.apana.org.au/~herbert/dash/files
 #diffutils-url = http://ftp.gnu.org/gnu/diffutils
-#file-url = ftp://ftp.astron.com/pub/file
+#file-url = http://ftp.astron.com/pub/file
 #findutils-url = http://ftp.gnu.org/gnu/findutils
 #flock-url = https://github.com/discoteq/flock/releases
 #gawk-url = http://ftp.gnu.org/gnu/gawk
@@ -35,12 +35,12 @@
 #gmp-url = https://gmplib.org/download/gmp
 #grep-url = http://ftp.gnu.org/gnu/grep
 #gzip-url = http://akhlaghi.org/src
-#isl-url = ftp://gcc.gnu.org/pub/gcc/infrastructure
+#isl-url = http://gcc.gnu.org/pub/gcc/infrastructure
 #less-url = http://www.greenwoodsoftware.com/less/
 #libiconv-url = https://ftp.gnu.org/pub/gnu/libiconv
 #libtool-url = http://ftp.gnu.org/gnu/libtool
 #libunistring-url = http://ftp.gnu.org/gnu/libunistring
-#libxml2-url = ftp://xmlsoft.org/libxml2
+#libxml2-url = https://download.gnome.org/sources/libxml2
 #lzip-url = https://download.savannah.gnu.org/releases/lzip/
 #m4-url = http://akhlaghi.org/maneage-software
 #make-url = http://akhlaghi.org/src
@@ -146,7 +146,7 @@
 #util-linux-url = https://mirrors.edge.kernel.org/pub/linux/utils/util-linux/v2.40
 #valgrind-url = https://sourceware.org/pub/valgrind
 #vim-url = ftp://ftp.vim.org/pub/vim/unix
-#wcslib-url = ftp://ftp.atnf.csiro.au/pub/software/wcslib
+#wcslib-url = https://www.atnf.csiro.au/computing/software/wcs/wcslib-releases
 #xlsxio-url = https://github.com/brechtsanders/xlsxio/archive
 #yaml-url = pyyaml.org/download/libyaml
 
diff --git a/reproduce/software/config/versions.conf b/reproduce/software/config/versions.conf
index 166e8ff..db5ac8e 100644
--- a/reproduce/software/config/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -17,38 +17,39 @@
 # --------------------------------------------------------------
 #
 # CLASS:BASIC (important identifier for 'awk'; don't modify this line)
-binutils-version = 2.43.1
+bash-version = 5.3.9
+binutils-version = 2.45.1
 bison-version = 3.8.2
-coreutils-version = 9.6
-curl-version = 8.11.1
-dash-version = 0.5.12
-diffutils-version = 3.10
+coreutils-version = 9.9
+curl-version = 8.17.0
+diffutils-version = 3.12
 file-version = 5.46
 findutils-version = 4.10.0
 flock-version = 0.4.0
-gawk-version = 5.3.1
-gcc-version = 14.2.0
-gettext-version = 0.23.1
-git-version = 2.48.1
+gawk-version = 5.3.2
+gcc-version = 15.2.0
+gettext-version = 0.26
+git-version = 2.52.0
 gmp-version = 6.3.0
-grep-version = 3.11
-gzip-version = 1.13
+grep-version = 3.12
+gzip-version = 1.14
 help2man-version = 1.49.3
 isl-version = 0.27
-less-version = 668
+less-version = 685
 libiconv-version = 1.18
 libtool-version = 2.5.4
-libunistring-version = 1.3
-libxml2-version = 2.13.5
+libunistring-version = 1.4.1
+libxml2-version = 2.15.1
 lzip-version = 1.25
+m4-version = 1.4.20
 make-version = 4.4.1
 mpc-version = 1.3.1
-mpfr-version = 4.2.1
-nano-version = 8.3
-openssl-version = 3.4.0
-perl-version = 5.40.1
+mpfr-version = 4.2.2
+nano-version = 8.7
+openssl-version = 3.6.0
+perl-version = 5.42.0
 podlators-version = 6.0.2
-readline-version = 8.2.13
+readline-version = 8.3.3
 sed-version = 4.9
 tar-version = 1.35
 texinfo-version = 7.2
@@ -86,6 +87,15 @@ certpem-version = 2025-02-10
 # supported.
 patchelf-version = 0.13
 
+# Dash
+# ----
+#
+# Dash 0.5.13.1 causes the build of pkg-config to put the building of
+# Maneage within apptainer to go into the background! Forcing the user to
+# run 'fg' to continue the build. When updating to a later version, be
+# careful about this: that it does not cause this issue.
+dash-version = 0.5.12
+
 # Not working with C23
 # --------------------
 #
@@ -96,8 +106,6 @@ patchelf-version = 0.13
 # '-std=c17' and then try the build. If it works, move the software back up
 # to the main list before the commit.
 ncurses-version = 6.5
-bash-version = 5.2.37
-m4-version = 1.4.19
 pkgconfig-version = 0.29.2
 
 
@@ -123,7 +131,7 @@ automake-version = 1.17
 boost-version = 1.87.0
 cairo-version = 1.16.0
 cdsclient-version = 3.84
-cfitsio-version = 4.5.0
+cfitsio-version = 4.6.3
 cmake-version = 3.31.5
 eigen-version = 3.4.0
 emacs-version = 28.1
@@ -134,8 +142,8 @@ freetype-version = 2.13.3
 gdb-version = 11.1
 ghostscript-fonts-gnu-version = 6.0
 ghostscript-fonts-std-version = 8.11
-ghostscript-version = 10.04.0
-gnuastro-version = 0.23
+ghostscript-version = 10.06.0
+gnuastro-version = 0.24
 gperf-version = 3.1
 gsl-version = 2.8
 icu-version = 70.1
@@ -169,10 +177,10 @@ sextractor-version = 2.25.0
 swarp-version = 2.41.5
 swig-version = 4.0.2
 tides-version = 2.0
-util-linux-version = 2.40.4
+util-linux-version = 2.41.3
 valgrind-version = 3.18.1
 vim-version = 9.0
-wcslib-version = 8.4
+wcslib-version = 8.5
 xlsxio-version = 0.2.21
 yaml-version = 0.2.5
 
diff --git a/reproduce/software/make/basic.mk b/reproduce/software/make/basic.mk
index 4b18c29..5a7024e 100644
--- a/reproduce/software/make/basic.mk
+++ b/reproduce/software/make/basic.mk
@@ -344,24 +344,22 @@ $(ibidir)/zlib-$(zlib-version): | $(ibdir) $(ildir) $(lockdir)
 	echo "Zlib $(zlib-version)" > $@
 
 # GNU Tar: When built statically, tar gives a segmentation fault on
-# unpacking Bash. So we'll build it dynamically. Note that technically, zip
-# and unzip aren't dependencies of Tar, but for a clean build, we'll set
-# Tar to be the last compression-related software (the first-set of
-# software to be built).
+# unpacking Bash. So we'll build it dynamically.
 $(ibidir)/tar-$(tar-version): \
               $(ibidir)/xz-$(xz-version) \
               $(ibidir)/gzip-$(gzip-version) \
               $(ibidir)/zlib-$(zlib-version) \
               $(ibidir)/bzip2-$(bzip2-version)
 
-#	Since all later programs depend on Tar, the configuration will hit
-#	a bottleneck here: only making Tar. So its more efficient to built
-#	it on multiple threads (even when the user's Make doesn't pass down
-#	the number of threads).
+#	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.
 	$(call unsafe-config)
 	tarball=tar-$(tar-version).tar.lz
 	$(call import-source, $(tar-url), $(tar-checksum))
-	$(call gbuild, tar-$(tar-version), , , -j$(numthreads) V=1)
+	$(call gbuild, tar-$(tar-version), , \
+	               --disable-nls am_cv_func_iconv=no, \
+	               -j$(numthreads) V=1)
 	echo "GNU Tar $(tar-version)" > $@
 
 
@@ -540,6 +538,7 @@ $(ibidir)/readline-$(readline-version): \
 #       pname=bash50-$(printf "%03d" $i); \
 #       wget http://ftp.gnu.org/gnu/bash/bash-5.0-patches/$pname -O ../$pname;\
 #       patch -p0 -i ../$pname; \
+#       rm ../$pname; \
 #     done
 #   $ cd ..
 #   $ mv bash-5.0 bash-5.0.$number
@@ -565,7 +564,7 @@ $(ibidir)/bash-$(bash-version): \
 	if [ "x$(static_build)" = xyes ]; then stopt="--enable-static-link"
 	else                                   stopt=""
 	fi;
-	export CFLAGS="$$CFLAGS -std=gnu17 \
+	export CFLAGS="$$CFLAGS \
 	               -DDEFAULT_PATH_VALUE='\"$(ibdir)\"' \
 	               -DSTANDARD_UTILS_PATH='\"$(ibdir)\"'  \
 	               -DSYS_BASHRC='\"$(BASH_ENV)\"' "
@@ -1065,10 +1064,6 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
 	               -j$(numthreads) V=1)
 	echo "GNU Grep $(grep-version)" > $@
 
-# M4 doesn't depend on PatchELF, but just to be consistent with the
-# levels/phases introduced here (where the compressors are level 1,
-# PatchELF is level 2, and ...), we'll set it as a dependency.
-#
 # The '--with-syscmd-shell' is used as the default shell and if not given,
 # 'm4' will use '/bin/sh' (which is not under Maneage control and can cause
 # problems in 'high-level.mk' because it closes off the system's
@@ -1076,10 +1071,9 @@ $(ibidir)/grep-$(grep-version): $(ibidir)/coreutils-$(coreutils-version)
 # library, the high-level programs will not be built). We are setting this
 # default shell to Dash because M4 is built before our own Bash. Recall
 # that Dash is built before we enter this Makefile.
-$(ibidir)/m4-$(m4-version): $(ibidir)/patchelf-$(patchelf-version)
+$(ibidir)/m4-$(m4-version): $(ibidir)/libiconv-$(libiconv-version)
 	tarball=m4-$(m4-version).tar.lz
 	$(call import-source, $(m4-url), $(m4-checksum))
-	export CFLAGS="-std=gnu17 $$CFLAGS"
 	$(call gbuild, m4-$(m4-version), static, \
 	               --with-syscmd-shell=$(ibdir)/dash, \
 	               -j$(numthreads) V=1)
diff --git a/reproduce/software/make/high-level.mk b/reproduce/software/make/high-level.mk
index 67ca8b6..685715f 100644
--- a/reproduce/software/make/high-level.mk
+++ b/reproduce/software/make/high-level.mk
@@ -731,7 +731,8 @@ $(ibidir)/libtiff-$(libtiff-version): $(ibidir)/libjpeg-$(libjpeg-version)
 	$(call gbuild, libtiff-$(libtiff-version), static, \
 	               --disable-jbig \
 	               --disable-webp \
-	               --disable-zstd)
+	               --disable-zstd \
+	               --disable-libdeflate )
 	echo "Libtiff $(libtiff-version)" > $@
 
 $(ibidir)/libtirpc-$(libtirpc-version):
@@ -1186,6 +1187,14 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 	tarball=ghostscript-$(ghostscript-version).tar.lz
 	$(call import-source, $(ghostscript-url), $(ghostscript-checksum))
 
+#	On macOS we use the system compiler and linker. The system linker
+#	there doesn't support '--copy-dt-needed-entries', while the one on
+#	Linux crashes if we remove it. So we only activate it on macOS.
+	ldflags=""
+	if [ x$(on_mac_os) = xno ]; then
+	     ldflags="LDFLAGS=-Wl,--copy-dt-needed-entries"
+	fi
+
 #	Unpack it and configure Ghostscript. The option
 #	'-DPNG_ARM_NEON_OPT=0' prevents an arm64 'neon' library from being
 #	required at compile time.
@@ -1193,13 +1202,13 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 	tar -xf $(tdir)/$$tarball --no-same-owner --no-same-permissions
 	cd ghostscript-$(ghostscript-version)
 	$(shsrcdir)/prep-source.sh $(ibdir)
-	./configure --prefix=$(idir) \
+	./configure $$ldflags \
 	            --disable-cups \
+	            --prefix=$(idir) \
 	            --enable-dynamic \
 	            --disable-compile-inits \
-		    --disable-hidden-visibility \
-		    CFLAGS="-DPNG_ARM_NEON_OPT=0" \
-		    LDFLAGS=-Wl,--copy-dt-needed-entries
+	            --disable-hidden-visibility \
+	            CFLAGS="-DPNG_ARM_NEON_OPT=0"
 
 #	Build and install the program and the shared libraries.
 	make    V=1 -j$(numthreads)
@@ -1224,17 +1233,24 @@ $(ibidir)/ghostscript-$(ghostscript-version): \
 	rm -rf ghostscript-$(ghostscript-version)
 	echo "GPL Ghostscript $(ghostscript-version)" > $@
 
+# Gnuastro can optionally depend on libgit2, but it is not included as a
+# dependency here for the two reasons below. If you would like to have it,
+# add it as a dependency (its build instruction and dependencies are here
+# already) and remove the '--without-libgit2' option in the recipe).
+#   - Within Maneage, we have everything under Git already and users are
+#     expected to include the version in all their products.
+#   - libgit2 can only be built with CMake (which takes extremely long to
+#     compile: possibly even longer than GCC!).
 $(ibidir)/gnuastro-$(gnuastro-version): \
                    $(ibidir)/gsl-$(gsl-version) \
                    $(ibidir)/wcslib-$(wcslib-version) \
                    $(ibidir)/libjpeg-$(libjpeg-version) \
                    $(ibidir)/libtiff-$(libtiff-version) \
-                   $(ibidir)/libgit2-$(libgit2-version) \
                    $(ibidir)/ghostscript-$(ghostscript-version)
 	tarball=gnuastro-$(gnuastro-version).tar.lz
 	$(call import-source, $(gnuastro-url), $(gnuastro-checksum))
-	$(call gbuild, gnuastro-$(gnuastro-version), static, , \
-	               -j$(numthreads))
+	$(call gbuild, gnuastro-$(gnuastro-version), static, \
+	               --without-libgit2, -j$(numthreads))
 	cp $(dtexdir)/gnuastro.tex $(ictdir)/
 	echo "GNU Astronomy Utilities $(gnuastro-version) \citep{gnuastro}" > $@
 
@@ -1720,6 +1736,12 @@ $(ibidir)/util-linux-$(util-linux-version): \
 	sed -e's|UL_BUILD_INIT(\[mkswap\], \[yes\])|UL_BUILD_INIT(\[mkswap\], \[no\])|' \
 	    -i configure.ac
 
+#	'autogen.sh' checks for dependencies, but 'flex' (that is not built
+#	in Maneage) is not needed when compiling from tarball (see:
+#	https://github.com/util-linux/util-linux/pull/2531#issuecomment-1798020594)
+	sed -i '/flex/d' autogen.sh
+	./autogen.sh
+
 #	Having updated 'configure.ac', we need to re-generate the
 #	'./configure' script with 'autoreconf' (which is part of Autoconf
 #	and needs Automake; hence why they are dependencies.
diff --git a/reproduce/software/shell/apptainer-README.md b/reproduce/software/shell/apptainer-README.md
index a7826ec..49ce82f 100644
--- a/reproduce/software/shell/apptainer-README.md
+++ b/reproduce/software/shell/apptainer-README.md
@@ -47,7 +47,7 @@ software environment) to easily move it from one computer to another.
       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
+ 3. To execute your project remove 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`.
 
diff --git a/reproduce/software/shell/apptainer.sh b/reproduce/software/shell/apptainer.sh
index c581ade..51b36db 100755
--- a/reproduce/software/shell/apptainer.sh
+++ b/reproduce/software/shell/apptainer.sh
@@ -291,10 +291,11 @@ else
     # necessary tools.
     if [ -f $base_name ]; then
         if [ $quiet = 0 ]; then
-            printf "$scriptname: info: base OS docker image ('$base_name') "
-            printf "already exists and will be used. If you want to build a "
-            printf "new base OS image, give a new name to '--base-name'. "
-            printf "To remove this message run with '--quiet'\n"
+            printf "$scriptname: info: base OS apptainer image "
+            printf "('$base_name') already exists and will be used. "
+            printf "If you want to build a new base OS image, give "
+            printf "a new name to '--base-name'. To remove this "
+            printf "message run with '--quiet'\n"
         fi
     else
 
diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index a409920..29b0ea6 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1891,9 +1891,10 @@ ______________________________________________________
 !!!!!!!!!!!!!!!        Warning        !!!!!!!!!!!!!!!!
 
 TeX Live couldn't be installed during the configuration (probably because
-there were downloading problems). TeX Live is only necessary in making the
-final PDF (which is only done after all the analysis has been complete). It
-is not used at all during the analysis.
+there were downloading problems, or you used the '--offline' option). TeX
+Live is only necessary in making the final PDF (which is only done after
+all the analysis has been complete). It is not used at all during the
+analysis.
 
 Therefore, if you don't need the final PDF, and just want to do the
 analysis, you can safely ignore this warning and continue.
diff --git a/reproduce/software/shell/prep-source.sh b/reproduce/software/shell/prep-source.sh
index dcdc472..2545460 100755
--- a/reproduce/software/shell/prep-source.sh
+++ b/reproduce/software/shell/prep-source.sh
@@ -77,6 +77,20 @@ fi
 if [ -f "$bindir/bash" ]; then shpath="$bindir"/bash
 else                           shpath="$bindir"/dash
 fi
+
+# On MacOS the syntax for 'stat' is a bit different, so if we are using the
+# system one on mac we need a specific syntax. The one installed by maneage
+# instead uses the ordinary Linux syntax.
+if [ -f "$bindir/stat" ] || [ x"$on_mac_os" = xno ]; then
+  format="--format %a"
+else
+  format="-f %OLp"
+fi
+
+# On MacOS 'touch' wants the time expressed according to ISO8601 with a
+# precision up to the seconds. We then use 'sed' to remove the information
+# regarding the timezone, as the format is not accepted by 'touch'.
+# LCTYPE and LANG are also required on macos systems by sed.
 grep -I -r -e'/bin/sh' $(pwd)/* \
     | sed -e's|:|\t|' \
     | awk 'BEGIN{FS="\t"}{print $1}' \
@@ -84,8 +98,10 @@ grep -I -r -e'/bin/sh' $(pwd)/* \
     | uniq \
     | while read filename; do \
          tmp="$filename".tmp; \
-         origtime="$(date -R -r "$filename")"; \
-         origperm=$(stat -c '%a' "$filename"); \
+         origtimex="$(date -Iseconds -r "$filename")"; \
+         origtime=$(echo $origtimex | sed 's/.\{6\}$//'); \
+         origperm=$(stat $format "$filename"); \
+         LC_CTYPE=C; LANG=C; \
          sed -e's|/bin/sh|'"$shpath"'|g' "$filename" > "$tmp"; \
          mv "$tmp" "$filename"; \
          chmod $origperm "$filename"; \
diff --git a/reproduce/software/shell/tarball-prepare.sh b/reproduce/software/shell/tarball-prepare.sh
index 8e30931..4d6d1e2 100755
--- a/reproduce/software/shell/tarball-prepare.sh
+++ b/reproduce/software/shell/tarball-prepare.sh
@@ -51,6 +51,9 @@ basedir=$PWD
 scriptname=$0
 
 
+
+
+
 # The --help output
 print_help() {
     cat <<EOF