diff --git a/pkgs/applications/networking/sync/rsync/default.nix b/pkgs/applications/networking/sync/rsync/default.nix
index 5216617bf4d1..555fb68416b8 100644
--- a/pkgs/applications/networking/sync/rsync/default.nix
+++ b/pkgs/applications/networking/sync/rsync/default.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , perl
 , libiconv
 , zlib
@@ -28,7 +29,7 @@ stdenv.mkDerivation rec {
     hash = "sha256-c5nppnCMMtZ4pypjIZ6W8jvgviM25Q/RNISY0HBB35A=";
   };
 
-  nativeBuildInputs = [ perl ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook perl ];
 
   buildInputs = [ libiconv zlib popt ]
     ++ lib.optional enableACLs acl
diff --git a/pkgs/development/libraries/c-ares/default.nix b/pkgs/development/libraries/c-ares/default.nix
index 87b86036cff2..e0bc7941b39e 100644
--- a/pkgs/development/libraries/c-ares/default.nix
+++ b/pkgs/development/libraries/c-ares/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, writeTextDir
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook
 , withCMake ? true, cmake
 
 # sensitive downstream packages
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" "man" ];
 
-  nativeBuildInputs = lib.optionals withCMake [ cmake ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ] ++ lib.optionals withCMake [ cmake ];
 
   cmakeFlags = [] ++ lib.optionals stdenv.hostPlatform.isStatic [
     "-DCARES_SHARED=OFF"
diff --git a/pkgs/development/libraries/expat/default.nix b/pkgs/development/libraries/expat/default.nix
index 9944277e946b..a26fd46abfde 100644
--- a/pkgs/development/libraries/expat/default.nix
+++ b/pkgs/development/libraries/expat/default.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 # for passthru.tests
 , python3
 , perlPackages
@@ -29,6 +30,7 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   strictDeps = true;
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
 
   outputs = [ "out" "dev" ]; # TODO: fix referrers
   outputBin = "dev";
diff --git a/pkgs/development/libraries/gdbm/default.nix b/pkgs/development/libraries/gdbm/default.nix
index e1a3def0ba42..d6ed7d32e701 100644
--- a/pkgs/development/libraries/gdbm/default.nix
+++ b/pkgs/development/libraries/gdbm/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl }:
+{ stdenv, lib, fetchurl, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "gdbm";
@@ -9,6 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-dLEIHSH/8TrkvXwW5dblBKTCb3zeHcoNljpIQXS7ys0=";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   doCheck = true; # not cross;
 
   # Linking static stubs on cygwin requires correct ordering.
diff --git a/pkgs/development/libraries/gettext/default.nix b/pkgs/development/libraries/gettext/default.nix
index 29c20d37ecf8..7a0d7a3ee667 100644
--- a/pkgs/development/libraries/gettext/default.nix
+++ b/pkgs/development/libraries/gettext/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, lib, fetchurl, libiconv, bash
+{ stdenv, lib, fetchurl, libiconv, bash, updateAutotoolsGnuConfigScriptsHook
 }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
@@ -50,6 +50,9 @@ stdenv.mkDerivation rec {
   '';
 
   strictDeps = true;
+  nativeBuildInputs = [
+    updateAutotoolsGnuConfigScriptsHook
+  ];
   buildInputs = lib.optionals (!stdenv.hostPlatform.isMinGW) [
     bash
   ]
diff --git a/pkgs/development/libraries/kerberos/krb5.nix b/pkgs/development/libraries/kerberos/krb5.nix
index 9f3fbdbf7eb0..8dd68af4fd1d 100644
--- a/pkgs/development/libraries/kerberos/krb5.nix
+++ b/pkgs/development/libraries/kerberos/krb5.nix
@@ -74,6 +74,11 @@ stdenv.mkDerivation rec {
   postPatch = ''
     substituteInPlace config/shlib.conf \
         --replace "'ld " "'${stdenv.cc.targetPrefix}ld "
+  ''
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  + ''
+    substituteInPlace ./config/config.guess --replace-fail /usr/bin/uname uname
   '';
 
   libFolders = [ "util" "include" "lib" "build-tools" ];
diff --git a/pkgs/development/libraries/libev/default.nix b/pkgs/development/libraries/libev/default.nix
index 750cb3974cf7..aa9f078d42b0 100644
--- a/pkgs/development/libraries/libev/default.nix
+++ b/pkgs/development/libraries/libev/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook
 , # Note: -static hasn’t work on darwin
   static ? with stdenv.hostPlatform; isStatic && !isDarwin
 }:
@@ -17,6 +17,8 @@ stdenv.mkDerivation rec {
     sha256 = "1sjs4324is7fp21an4aas2z4dwsvs6z4xwrmp72vwpq1s6wbfzjh";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   configureFlags = lib.optional (static) "LDFLAGS=-static";
 
   meta = {
diff --git a/pkgs/development/libraries/libssh2/default.nix b/pkgs/development/libraries/libssh2/default.nix
index f7a51da9fa67..653575c5563b 100644
--- a/pkgs/development/libraries/libssh2/default.nix
+++ b/pkgs/development/libraries/libssh2/default.nix
@@ -15,6 +15,12 @@ stdenv.mkDerivation rec {
     ./CVE-2023-48795.patch
   ];
 
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  postPatch = ''
+    substituteInPlace ./config.guess --replace-fail /usr/bin/uname uname
+  '';
+
   outputs = [ "out" "dev" "devdoc" ];
 
   propagatedBuildInputs = [ openssl ]; # see Libs: in libssh2.pc
diff --git a/pkgs/development/libraries/libxcrypt/default.nix b/pkgs/development/libraries/libxcrypt/default.nix
index d71cb7027570..efd3acb643fb 100644
--- a/pkgs/development/libraries/libxcrypt/default.nix
+++ b/pkgs/development/libraries/libxcrypt/default.nix
@@ -15,6 +15,12 @@ stdenv.mkDerivation (finalAttrs: {
     hash = "sha256-5eH0yu4KAd4q7ibjE4gH1tPKK45nKHlm0f79ZeH9iUM=";
   };
 
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  postPatch = ''
+    substituteInPlace ./build-aux/m4-autogen/config.guess --replace-fail /usr/bin/uname uname
+  '';
+
   outputs = [
     "out"
     "man"
diff --git a/pkgs/development/libraries/lzo/default.nix b/pkgs/development/libraries/lzo/default.nix
index 480e2bb909cd..43d551819a65 100644
--- a/pkgs/development/libraries/lzo/default.nix
+++ b/pkgs/development/libraries/lzo/default.nix
@@ -1,4 +1,4 @@
-{lib, stdenv, fetchurl}:
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "lzo";
@@ -9,6 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "0wm04519pd3g8hqpjqhfr72q8qmbiwqaxcs3cndny9h86aa95y60";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   configureFlags = lib.optional (!stdenv.hostPlatform.isStatic) "--enable-shared" ;
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/mpdecimal/default.nix b/pkgs/development/libraries/mpdecimal/default.nix
index 514c61ffcb0c..687abab7d45b 100644
--- a/pkgs/development/libraries/mpdecimal/default.nix
+++ b/pkgs/development/libraries/mpdecimal/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl }:
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "mpdecimal";
@@ -10,6 +10,8 @@ stdenv.mkDerivation rec {
     hash = "sha256-lCRFwyRbInMP1Bpnp8XCMdEcsbmTa5wPdjNPt9C0Row=";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   configureFlags = [ "LD=${stdenv.cc.targetPrefix}cc" ];
 
   postInstall = ''
diff --git a/pkgs/development/libraries/ncurses/default.nix b/pkgs/development/libraries/ncurses/default.nix
index 141ebc857130..2a160c0abbca 100644
--- a/pkgs/development/libraries/ncurses/default.nix
+++ b/pkgs/development/libraries/ncurses/default.nix
@@ -2,6 +2,7 @@
 , stdenv
 , fetchurl
 , buildPackages
+, updateAutotoolsGnuConfigScriptsHook
 , ncurses
 , pkg-config
 , abiVersion ? "6"
@@ -68,6 +69,7 @@ stdenv.mkDerivation (finalAttrs: {
   strictDeps = true;
 
   nativeBuildInputs = [
+    updateAutotoolsGnuConfigScriptsHook
     pkg-config
   ] ++ lib.optionals (stdenv.buildPlatform != stdenv.hostPlatform) [
    # for `tic`, build already depends on for build `cc` so it's weird the build doesn't just build `tic`.
diff --git a/pkgs/development/libraries/nghttp2/default.nix b/pkgs/development/libraries/nghttp2/default.nix
index 5566b0c8f67d..0fe8f1d88d51 100644
--- a/pkgs/development/libraries/nghttp2/default.nix
+++ b/pkgs/development/libraries/nghttp2/default.nix
@@ -67,6 +67,12 @@ stdenv.mkDerivation rec {
     export TZDIR=${tzdata}/share/zoneinfo
   '';
 
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  postPatch = ''
+    substituteInPlace ./config.guess --replace-fail /usr/bin/uname uname
+  '';
+
   postInstall = lib.optionalString (enableApp) ''
     installShellCompletion --bash doc/bash_completion/{h2load,nghttp,nghttpd,nghttpx}
   '' + lib.optionalString (!enableApp) ''
diff --git a/pkgs/development/libraries/pcre2/default.nix b/pkgs/development/libraries/pcre2/default.nix
index c30a3c379d1d..3450f910effe 100644
--- a/pkgs/development/libraries/pcre2/default.nix
+++ b/pkgs/development/libraries/pcre2/default.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , withJitSealloc ? true
 }:
 
@@ -13,6 +14,8 @@ stdenv.mkDerivation rec {
     hash = "sha256-4qU5hP8LB9/bWuRIa7ubIcyo598kNAlsyb8bcow1C8s=";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   postPatch = ''
     # Fix jit autodetection:
     #   https://github.com/PCRE2Project/pcre2/pull/396
diff --git a/pkgs/development/libraries/popt/default.nix b/pkgs/development/libraries/popt/default.nix
index fdccb4d09336..e97629b0dfd0 100644
--- a/pkgs/development/libraries/popt/default.nix
+++ b/pkgs/development/libraries/popt/default.nix
@@ -2,6 +2,7 @@
 , stdenv
 , fetchurl
 , fetchpatch2
+, updateAutotoolsGnuConfigScriptsHook
 }:
 
 stdenv.mkDerivation rec {
@@ -13,6 +14,8 @@ stdenv.mkDerivation rec {
     sha256 = "sha256-wlpIOPyOTByKrLi9Yg7bMISj1jv4mH/a08onWMYyQPk=";
   };
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
+
   patches = lib.optionals stdenv.isCygwin [
     ./1.16-cygwin.patch
     ./1.16-vpath.patch
diff --git a/pkgs/development/libraries/readline/8.2.nix b/pkgs/development/libraries/readline/8.2.nix
index 72e3370576e7..7bf5caf4060f 100644
--- a/pkgs/development/libraries/readline/8.2.nix
+++ b/pkgs/development/libraries/readline/8.2.nix
@@ -1,5 +1,6 @@
 { lib, stdenv
 , fetchpatch, fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , ncurses, termcap
 , curses-library ?
     if stdenv.hostPlatform.isWindows
@@ -20,6 +21,7 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
   propagatedBuildInputs = [ curses-library ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
 
   patchFlags = [ "-p0" ];
 
diff --git a/pkgs/development/libraries/sqlite/default.nix b/pkgs/development/libraries/sqlite/default.nix
index fe39cac8a25f..1932d659d180 100644
--- a/pkgs/development/libraries/sqlite/default.nix
+++ b/pkgs/development/libraries/sqlite/default.nix
@@ -1,4 +1,5 @@
 { lib, stdenv, fetchurl, zlib, readline, ncurses
+, updateAutotoolsGnuConfigScriptsHook
 
 # for tests
 , python3Packages, sqldiff, sqlite-analyzer, tracker
@@ -27,6 +28,7 @@ stdenv.mkDerivation rec {
   outputs = [ "bin" "dev" "out" ];
   separateDebugInfo = stdenv.isLinux;
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
   buildInputs = [ zlib ] ++ lib.optionals interactive [ readline ncurses ];
 
   # required for aarch64 but applied for all arches for simplicity
diff --git a/pkgs/development/tools/build-managers/gnumake/default.nix b/pkgs/development/tools/build-managers/gnumake/default.nix
index 774ea50f8623..7c075b7d8b8b 100644
--- a/pkgs/development/tools/build-managers/gnumake/default.nix
+++ b/pkgs/development/tools/build-managers/gnumake/default.nix
@@ -1,6 +1,7 @@
 { lib
 , stdenv
 , fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , guileSupport ? false, guile
 # avoid guile depend on bootstrap to prevent dependency cycles
 , inBootstrap ? false
@@ -31,7 +32,7 @@ stdenv.mkDerivation rec {
     ./0002-remove-impure-dirs.patch
   ];
 
-  nativeBuildInputs = lib.optionals guileEnabled [ pkg-config ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ] ++ lib.optionals guileEnabled [ pkg-config ];
   buildInputs = lib.optionals guileEnabled [ guile ];
 
   configureFlags = lib.optional guileEnabled "--with-guile"
diff --git a/pkgs/development/tools/misc/automake/automake-1.16.x.nix b/pkgs/development/tools/misc/automake/automake-1.16.x.nix
index 0d9572c6f314..20fe31ef6cd7 100644
--- a/pkgs/development/tools/misc/automake/automake-1.16.x.nix
+++ b/pkgs/development/tools/misc/automake/automake-1.16.x.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, perl, autoconf }:
+{ lib, stdenv, fetchurl, perl, autoconf, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "automake";
@@ -10,7 +10,7 @@ stdenv.mkDerivation rec {
   };
 
   strictDeps = true;
-  nativeBuildInputs = [ autoconf perl ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook autoconf perl ];
   buildInputs = [ autoconf ];
 
   setupHook = ./setup-hook.sh;
diff --git a/pkgs/development/tools/misc/dejagnu/default.nix b/pkgs/development/tools/misc/dejagnu/default.nix
index 5c7720a2024b..55581aedce60 100644
--- a/pkgs/development/tools/misc/dejagnu/default.nix
+++ b/pkgs/development/tools/misc/dejagnu/default.nix
@@ -1,4 +1,4 @@
-{ fetchurl, lib, stdenv, expect, makeWrapper }:
+{ fetchurl, lib, stdenv, expect, makeWrapper, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "dejagnu";
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "1qx2cv6qkxbiqg87jh217jb62hk3s7dmcs4cz1llm2wmsynfznl7";
   };
 
-  nativeBuildInputs = [ makeWrapper ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook makeWrapper ];
   buildInputs = [ expect ];
 
   # dejagnu-1.6.3 can't successfully run tests in source tree:
diff --git a/pkgs/development/tools/misc/gnum4/default.nix b/pkgs/development/tools/misc/gnum4/default.nix
index 66de4ebf8b02..5dea7f059557 100644
--- a/pkgs/development/tools/misc/gnum4/default.nix
+++ b/pkgs/development/tools/misc/gnum4/default.nix
@@ -16,12 +16,17 @@ stdenv.mkDerivation rec {
 
   # https://gitweb.gentoo.org/repo/gentoo.git/tree/sys-devel/m4/m4-1.4.19-r1.ebuild
   patches = lib.optional stdenv.hostPlatform.isLoongArch64 ./loong-fix-build.patch;
-  postPatch = if stdenv.hostPlatform.isLoongArch64 then ''
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  postPatch = ''
+    substituteInPlace ./build-aux/config.guess --replace-fail /usr/bin/uname uname
+  '' + lib.optionalString stdenv.hostPlatform.isLoongArch64 ''
     touch ./aclocal.m4 ./lib/config.hin ./configure ./doc/stamp-vti || die
     find . -name Makefile.in -exec touch {} + || die
-  '' else null;
+  '';
 
   strictDeps = true;
+
   enableParallelBuilding = true;
 
   doCheck = false;
diff --git a/pkgs/development/tools/misc/libtool/libtool2.nix b/pkgs/development/tools/misc/libtool/libtool2.nix
index 259fb2b113c7..df07a2f6a5bf 100644
--- a/pkgs/development/tools/misc/libtool/libtool2.nix
+++ b/pkgs/development/tools/misc/libtool/libtool2.nix
@@ -1,5 +1,6 @@
 { lib, stdenv, fetchurl, m4
 , runtimeShell
+, updateAutotoolsGnuConfigScriptsHook
 , file
 }:
 
@@ -38,7 +39,7 @@ stdenv.mkDerivation rec {
   # As libtool is an early bootstrap dependency try hard not to
   # add autoconf and automake or help2man dependencies here. That way we can
   # avoid pulling in perl and get away with just an `m4` depend.
-  nativeBuildInputs = [ m4 file ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook m4 file ];
   propagatedBuildInputs = [ m4 file ];
 
   # Don't fixup "#! /bin/sh" in Libtool, otherwise it will use the
diff --git a/pkgs/development/tools/misc/pkg-config/default.nix b/pkgs/development/tools/misc/pkg-config/default.nix
index 663f3184b221..599d28285809 100644
--- a/pkgs/development/tools/misc/pkg-config/default.nix
+++ b/pkgs/development/tools/misc/pkg-config/default.nix
@@ -19,9 +19,14 @@ stdenv.mkDerivation rec {
     ++ lib.optional stdenv.isCygwin ./2.36.3-not-win32.patch;
 
   # These three tests fail due to a (desired) behavior change from our ./requires-private.patch
-  postPatch = if vanilla then null else ''
-    rm -f check/check-requires-private check/check-gtk check/missing
-  '';
+  postPatch =
+    # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+    # necessary for FreeBSD code path in configure
+    ''
+      substituteInPlace ./config.guess ./glib/config.guess --replace-fail /usr/bin/uname uname
+    '' + lib.optionalString (!vanilla) ''
+      rm -f check/check-requires-private check/check-gtk check/missing
+    '';
 
   buildInputs = [ libiconv ];
 
diff --git a/pkgs/development/tools/misc/texinfo/common.nix b/pkgs/development/tools/misc/texinfo/common.nix
index d1f8cc582543..11144d7581a5 100644
--- a/pkgs/development/tools/misc/texinfo/common.nix
+++ b/pkgs/development/tools/misc/texinfo/common.nix
@@ -1,7 +1,7 @@
 { version, sha256, patches ? [] }:
 
 { lib, stdenv, buildPackages, fetchurl, perl, libintl, bash
-, gnulib, gawk, freebsd, libiconv
+, updateAutotoolsGnuConfigScriptsHook, gnulib, gawk, freebsd, libiconv
 
 # we are a dependency of gcc, this simplifies bootstraping
 , interactive ? false, ncurses, procps
@@ -49,6 +49,7 @@ stdenv.mkDerivation {
   # A native compiler is needed to build tools needed at build time
   depsBuildBuild = [ buildPackages.stdenv.cc perl ];
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
   buildInputs = [ bash libintl ]
     ++ optionals stdenv.isSunOS [ libiconv gawk ]
     ++ optional interactive ncurses;
diff --git a/pkgs/servers/x11/xorg/overrides.nix b/pkgs/servers/x11/xorg/overrides.nix
index a6d7d7e6a7f0..cd7e116c17d5 100644
--- a/pkgs/servers/x11/xorg/overrides.nix
+++ b/pkgs/servers/x11/xorg/overrides.nix
@@ -3,7 +3,7 @@
   automake, autoconf, libiconv, libtool, intltool, gettext, python3, perl,
   freetype, tradcpp, fontconfig, meson, ninja, ed, fontforge,
   libGL, spice-protocol, zlib, libGLU, dbus, libunwind, libdrm, netbsd,
-  ncompress,
+  ncompress, updateAutotoolsGnuConfigScriptsHook,
   mesa, udev, bootstrap_cmds, bison, flex, clangStdenv, autoreconfHook,
   mcpp, libepoxy, openssl, pkg-config, llvm, libxslt, libxcrypt, hwdata,
   ApplicationServices, Carbon, Cocoa, Xplugin,
@@ -906,6 +906,7 @@ self: super:
 
   lndir = super.lndir.overrideAttrs (attrs: {
     buildInputs = [];
+    nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
     preConfigure = ''
       export XPROTO_CFLAGS=" "
       export XPROTO_LIBS=" "
diff --git a/pkgs/shells/bash/5.nix b/pkgs/shells/bash/5.nix
index cdce3667c5cd..25798533113c 100644
--- a/pkgs/shells/bash/5.nix
+++ b/pkgs/shells/bash/5.nix
@@ -2,6 +2,7 @@
 , stdenv
 , buildPackages
 , fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , bison
 , util-linux
 
@@ -97,7 +98,7 @@ stdenv.mkDerivation rec {
   strictDeps = true;
   # Note: Bison is needed because the patches above modify parse.y.
   depsBuildBuild = [ buildPackages.stdenv.cc ];
-  nativeBuildInputs = [ bison ]
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook bison ]
     ++ lib.optional withDocs texinfo
     ++ lib.optional stdenv.hostPlatform.isDarwin stdenv.cc.bintools;
 
diff --git a/pkgs/tools/archivers/gnutar/default.nix b/pkgs/tools/archivers/gnutar/default.nix
index 34615d7e8bed..98f0b54e73fc 100644
--- a/pkgs/tools/archivers/gnutar/default.nix
+++ b/pkgs/tools/archivers/gnutar/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, autoreconfHook, acl, libintl }:
+{ lib, stdenv, fetchurl, autoreconfHook, updateAutotoolsGnuConfigScriptsHook, acl, libintl }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
 # cannot use fetchpatch! All mutable patches (generated by GitHub or
@@ -30,7 +30,8 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "info" ];
 
-  nativeBuildInputs = lib.optional stdenv.isDarwin autoreconfHook;
+  nativeBuildInputs = lib.optional stdenv.isDarwin autoreconfHook
+    ++ lib.optional (!stdenv.isDarwin) updateAutotoolsGnuConfigScriptsHook;
   # Add libintl on Darwin specifically as it fails to link (or skip)
   # NLS on it's own:
   #  "_libintl_textdomain", referenced from:
diff --git a/pkgs/tools/archivers/sharutils/default.nix b/pkgs/tools/archivers/sharutils/default.nix
index 5c84e596531c..2a656a9dd327 100644
--- a/pkgs/tools/archivers/sharutils/default.nix
+++ b/pkgs/tools/archivers/sharutils/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, fetchpatch, gettext, coreutils }:
+{ lib, stdenv, fetchurl, fetchpatch, gettext, coreutils, updateAutotoolsGnuConfigScriptsHook }:
 
 stdenv.mkDerivation rec {
   pname = "sharutils";
@@ -13,6 +13,7 @@ stdenv.mkDerivation rec {
 
   # GNU Gettext is needed on non-GNU platforms.
   buildInputs = [ coreutils gettext ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
 
   # These tests try to hit /etc/passwd to find out your username if pass in a submitter
   # name on the command line. Since we block access to /etc/passwd on the Darwin sandbox
diff --git a/pkgs/tools/compression/gzip/default.nix b/pkgs/tools/compression/gzip/default.nix
index 56803742d605..05539050861f 100644
--- a/pkgs/tools/compression/gzip/default.nix
+++ b/pkgs/tools/compression/gzip/default.nix
@@ -1,6 +1,7 @@
 { lib, stdenv
 , fetchurl
 , makeWrapper
+, updateAutotoolsGnuConfigScriptsHook
 , xz
 , runtimeShellPackage
 }:
@@ -23,8 +24,8 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  buildInputs = [ runtimeShellPackage];
-  nativeBuildInputs = [ xz.bin makeWrapper ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook makeWrapper ];
+  buildInputs = [ runtimeShellPackage ];
 
   makeFlags = [
     "SHELL=/bin/sh"
diff --git a/pkgs/tools/compression/xz/default.nix b/pkgs/tools/compression/xz/default.nix
index 4431a178ac02..2a7ca487bcfd 100644
--- a/pkgs/tools/compression/xz/default.nix
+++ b/pkgs/tools/compression/xz/default.nix
@@ -29,6 +29,12 @@ stdenv.mkDerivation (finalAttrs: {
   enableParallelBuilding = true;
   doCheck = true;
 
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
+  postPatch = ''
+    substituteInPlace ./build-aux/config.guess --replace-fail /usr/bin/uname uname
+  '';
+
   preCheck = ''
     # Tests have a /bin/sh dependency...
     patchShebangs tests
diff --git a/pkgs/tools/misc/file/default.nix b/pkgs/tools/misc/file/default.nix
index 8cff5ccd70af..4aab839a8a56 100644
--- a/pkgs/tools/misc/file/default.nix
+++ b/pkgs/tools/misc/file/default.nix
@@ -1,4 +1,5 @@
 { lib, stdenv, fetchurl, file, zlib, libgnurx
+, updateAutotoolsGnuConfigScriptsHook
 , testers
 }:
 
@@ -30,7 +31,8 @@ stdenv.mkDerivation (finalAttrs: {
   strictDeps = true;
   enableParallelBuilding = true;
 
-  nativeBuildInputs = lib.optional (stdenv.hostPlatform != stdenv.buildPlatform) file;
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ]
+    ++ lib.optional (stdenv.hostPlatform != stdenv.buildPlatform) file;
   buildInputs = [ zlib ]
     ++ lib.optional stdenv.hostPlatform.isWindows libgnurx;
 
diff --git a/pkgs/tools/misc/findutils/default.nix b/pkgs/tools/misc/findutils/default.nix
index b3810892ce03..cfa4105cda0d 100644
--- a/pkgs/tools/misc/findutils/default.nix
+++ b/pkgs/tools/misc/findutils/default.nix
@@ -1,4 +1,5 @@
 { lib, stdenv, fetchurl
+, updateAutotoolsGnuConfigScriptsHook
 , coreutils
 }:
 
@@ -22,6 +23,7 @@ stdenv.mkDerivation rec {
 
   patches = [ ./no-install-statedir.patch ];
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
   buildInputs = [ coreutils ]; # bin/updatedb script needs to call sort
 
   # Since glibc-2.25 the i686 tests hang reliably right after test-sleep.
diff --git a/pkgs/tools/networking/curl/default.nix b/pkgs/tools/networking/curl/default.nix
index 0bd65a307b0b..918cb60848fb 100644
--- a/pkgs/tools/networking/curl/default.nix
+++ b/pkgs/tools/networking/curl/default.nix
@@ -65,7 +65,10 @@ stdenv.mkDerivation (finalAttrs: {
     ./8.7.1-compression-fix.patch
   ];
 
+  # this could be accomplished by updateAutotoolsGnuConfigScriptsHook, but that causes infinite recursion
+  # necessary for FreeBSD code path in configure
   postPatch = ''
+    substituteInPlace ./config.guess --replace-fail /usr/bin/uname uname
     patchShebangs scripts
   '';
 
diff --git a/pkgs/tools/text/diffutils/default.nix b/pkgs/tools/text/diffutils/default.nix
index 8c4a160d4b1e..6c1bc8bf01f1 100644
--- a/pkgs/tools/text/diffutils/default.nix
+++ b/pkgs/tools/text/diffutils/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, xz, coreutils ? null }:
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook, xz, coreutils ? null }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
 # cannot use fetchpatch! All mutable patches (generated by GitHub or
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "info" ];
 
-  nativeBuildInputs = [ (lib.getBin xz) ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook (lib.getBin xz) ];
   /* If no explicit coreutils is given, use the one from stdenv. */
   buildInputs = [ coreutils ];
 
diff --git a/pkgs/tools/text/gnugrep/default.nix b/pkgs/tools/text/gnugrep/default.nix
index 55e0a97f3594..7298fe881bea 100644
--- a/pkgs/tools/text/gnugrep/default.nix
+++ b/pkgs/tools/text/gnugrep/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, glibcLocales, fetchurl, pcre2, libiconv, perl, runtimeShellPackage }:
+{ lib, stdenv, updateAutotoolsGnuConfigScriptsHook, glibcLocales, fetchurl, pcre2, libiconv, perl, runtimeShellPackage }:
 
 # Note: this package is used for bootstrapping fetchurl, and thus
 # cannot use fetchpatch! All mutable patches (generated by GitHub or
@@ -26,6 +26,7 @@ stdenv.mkDerivation {
   nativeCheckInputs = [ perl glibcLocales ];
   outputs = [ "out" "info" ]; # the man pages are rather small
 
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook ];
   buildInputs = [ pcre2 libiconv runtimeShellPackage ];
 
   # cygwin: FAIL: multibyte-white-space
diff --git a/pkgs/tools/text/gnused/default.nix b/pkgs/tools/text/gnused/default.nix
index f493e4f358d6..bc736f418725 100644
--- a/pkgs/tools/text/gnused/default.nix
+++ b/pkgs/tools/text/gnused/default.nix
@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, perl }:
+{ lib, stdenv, fetchurl, updateAutotoolsGnuConfigScriptsHook, perl }:
 
 stdenv.mkDerivation rec {
   pname = "gnused";
@@ -11,7 +11,7 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "info" ];
 
-  nativeBuildInputs = [ perl ];
+  nativeBuildInputs = [ updateAutotoolsGnuConfigScriptsHook perl ];
   preConfigure = "patchShebangs ./build-aux/help2man";
 
   # Prevents attempts of running 'help2man' on cross-built binaries.