diff --git a/pkgs/tools/typesetting/asciidoc/default.nix b/pkgs/by-name/as/asciidoc/package.nix
similarity index 98%
rename from pkgs/tools/typesetting/asciidoc/default.nix
rename to pkgs/by-name/as/asciidoc/package.nix
index a301ee3827f0b..ef29ed7f27f77 100644
--- a/pkgs/tools/typesetting/asciidoc/default.nix
+++ b/pkgs/by-name/as/asciidoc/package.nix
@@ -9,12 +9,11 @@
   enableStandardFeatures ? false,
   sourceHighlight,
   highlight,
-  pygments,
   graphviz,
   texliveMinimal,
   dblatexFull,
   libxslt,
-  w3m,
+  w3m-batch,
   lynx,
   imagemagick,
   lilypond,
@@ -45,11 +44,7 @@
   enableQrcodeFilter ? false,
   qrencode,
   enableMatplotlibFilter ? false,
-  matplotlib,
-  numpy,
   enableAafigureFilter ? false,
-  aafigure,
-  recursive-pth-loader,
   # backends
   enableDeckjsBackend ? false,
   enableOdfBackend ? false,
@@ -61,6 +56,13 @@
 }:
 
 let
+  inherit (python3.pkgs)
+    pygments
+    matplotlib
+    numpy
+    aafigure
+    recursive-pth-loader
+    ;
 
   _enableDitaaFilter = (enableExtraPlugins && enableJava) || enableDitaaFilter;
   _enableMscgenFilter = enableExtraPlugins || enableMscgenFilter;
@@ -268,7 +270,7 @@ python3.pkgs.buildPythonApplication rec {
             -e "s|^XSLTPROC =.*|XSLTPROC = '${libxslt.bin}/bin/xsltproc'|" \
             -e "s|^DBLATEX =.*|DBLATEX = '${dblatexFull}/bin/dblatex'|" \
             ${lib.optionalString enableJava ''-e "s|^FOP =.*|FOP = '${fop}/bin/fop'|"''} \
-            -e "s|^W3M =.*|W3M = '${w3m}/bin/w3m'|" \
+            -e "s|^W3M =.*|W3M = '${w3m-batch}/bin/w3m'|" \
             -e "s|^LYNX =.*|LYNX = '${lynx}/bin/lynx'|" \
             -e "s|^XMLLINT =.*|XMLLINT = '${libxml2.bin}/bin/xmllint'|" \
             -e "s|^EPUBCHECK =.*|EPUBCHECK = '${epubcheck}/bin/epubcheck'|" \
diff --git a/pkgs/tools/admin/cdist/default.nix b/pkgs/by-name/cd/cdist/package.nix
similarity index 92%
rename from pkgs/tools/admin/cdist/default.nix
rename to pkgs/by-name/cd/cdist/package.nix
index 239e611e5b6aa..893438b6c7cab 100644
--- a/pkgs/tools/admin/cdist/default.nix
+++ b/pkgs/by-name/cd/cdist/package.nix
@@ -1,13 +1,10 @@
 {
   lib,
-  buildPythonApplication,
+  python3Packages,
   fetchFromGitea,
-  six,
-  sphinxHook,
-  sphinx-rtd-theme,
 }:
 
-buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "cdist";
   version = "7.0.0";
   format = "setuptools";
@@ -25,7 +22,7 @@ buildPythonApplication rec {
     hash = "sha256-lIx0RtGQJdY2e00azI9yS6TV+5pCegpKOOD0dQmgMqA=";
   };
 
-  nativeBuildInputs = [
+  nativeBuildInputs = with python3Packages; [
     six
     sphinxHook
     sphinx-rtd-theme
diff --git a/pkgs/tools/virtualization/cloud-init/0001-add-nixos-support.patch b/pkgs/by-name/cl/cloud-init/0001-add-nixos-support.patch
similarity index 100%
rename from pkgs/tools/virtualization/cloud-init/0001-add-nixos-support.patch
rename to pkgs/by-name/cl/cloud-init/0001-add-nixos-support.patch
diff --git a/pkgs/tools/virtualization/cloud-init/0002-fix-test-logs-on-nixos.patch b/pkgs/by-name/cl/cloud-init/0002-fix-test-logs-on-nixos.patch
similarity index 100%
rename from pkgs/tools/virtualization/cloud-init/0002-fix-test-logs-on-nixos.patch
rename to pkgs/by-name/cl/cloud-init/0002-fix-test-logs-on-nixos.patch
diff --git a/pkgs/tools/virtualization/cloud-init/default.nix b/pkgs/by-name/cl/cloud-init/package.nix
similarity index 100%
rename from pkgs/tools/virtualization/cloud-init/default.nix
rename to pkgs/by-name/cl/cloud-init/package.nix
diff --git a/pkgs/tools/filesystems/disorderfs/default.nix b/pkgs/by-name/di/disorderfs/package.nix
similarity index 95%
rename from pkgs/tools/filesystems/disorderfs/default.nix
rename to pkgs/by-name/di/disorderfs/package.nix
index e15225bc89de7..960a451763afb 100644
--- a/pkgs/tools/filesystems/disorderfs/default.nix
+++ b/pkgs/by-name/di/disorderfs/package.nix
@@ -5,7 +5,7 @@
   pkg-config,
   fuse,
   attr,
-  asciidoc,
+  asciidoc-full,
 }:
 
 stdenv.mkDerivation rec {
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [
     pkg-config
-    asciidoc
+    asciidoc-full
   ];
 
   buildInputs = [
diff --git a/pkgs/tools/games/gamemode/default.nix b/pkgs/by-name/ga/gamemode/package.nix
similarity index 97%
rename from pkgs/tools/games/gamemode/default.nix
rename to pkgs/by-name/ga/gamemode/package.nix
index 45122bf701b0b..ed512d32f76ac 100644
--- a/pkgs/tools/games/gamemode/default.nix
+++ b/pkgs/by-name/ga/gamemode/package.nix
@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchFromGitHub,
-  libgamemode32,
+  pkgsi686Linux,
   makeWrapper,
   meson,
   ninja,
@@ -49,7 +49,7 @@ stdenv.mkDerivation (finalAttrs: {
           ]
           ++ lib.optionals (stdenv.hostPlatform.system == "x86_64-linux") [
             # Support wrapping 32bit applications on a 64bit linux system
-            libgamemode32
+            pkgsi686Linux.gamemode.lib
           ]
         )
       }
diff --git a/pkgs/tools/games/gamemode/preload-nix-workaround.patch b/pkgs/by-name/ga/gamemode/preload-nix-workaround.patch
similarity index 100%
rename from pkgs/tools/games/gamemode/preload-nix-workaround.patch
rename to pkgs/by-name/ga/gamemode/preload-nix-workaround.patch
diff --git a/pkgs/tools/admin/ibmcloud-cli/default.nix b/pkgs/by-name/ib/ibmcloud-cli/package.nix
similarity index 98%
rename from pkgs/tools/admin/ibmcloud-cli/default.nix
rename to pkgs/by-name/ib/ibmcloud-cli/package.nix
index 6527ce2cd014e..1fea5163733b1 100644
--- a/pkgs/tools/admin/ibmcloud-cli/default.nix
+++ b/pkgs/by-name/ib/ibmcloud-cli/package.nix
@@ -1,11 +1,12 @@
 {
   lib,
-  stdenv,
+  stdenvNoCC,
   fetchurl,
   installShellFiles,
   writableTmpDirAsHomeHook,
 }:
 let
+  stdenv = stdenvNoCC;
   arch =
     with stdenv.hostPlatform;
     if isx86_64 then
diff --git a/pkgs/tools/admin/ibmcloud-cli/update.sh b/pkgs/by-name/ib/ibmcloud-cli/update.sh
similarity index 100%
rename from pkgs/tools/admin/ibmcloud-cli/update.sh
rename to pkgs/by-name/ib/ibmcloud-cli/update.sh
diff --git a/pkgs/tools/filesystems/kio-fuse/default.nix b/pkgs/by-name/ki/kio-fuse/package.nix
similarity index 91%
rename from pkgs/tools/filesystems/kio-fuse/default.nix
rename to pkgs/by-name/ki/kio-fuse/package.nix
index 3a34068662357..298c7b1ccc497 100644
--- a/pkgs/tools/filesystems/kio-fuse/default.nix
+++ b/pkgs/by-name/ki/kio-fuse/package.nix
@@ -4,8 +4,7 @@
   fetchgit,
   cmake,
   extra-cmake-modules,
-  wrapQtAppsHook,
-  kio,
+  libsForQt5,
   fuse3,
 }:
 
@@ -22,11 +21,11 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [
     cmake
     extra-cmake-modules
-    wrapQtAppsHook
+    libsForQt5.wrapQtAppsHook
   ];
 
   buildInputs = [
-    kio
+    libsForQt5.kio
     fuse3
   ];
 
diff --git a/pkgs/tools/typesetting/kramdown-asciidoc/Gemfile b/pkgs/by-name/kr/kramdown-asciidoc/Gemfile
similarity index 100%
rename from pkgs/tools/typesetting/kramdown-asciidoc/Gemfile
rename to pkgs/by-name/kr/kramdown-asciidoc/Gemfile
diff --git a/pkgs/tools/typesetting/kramdown-asciidoc/Gemfile.lock b/pkgs/by-name/kr/kramdown-asciidoc/Gemfile.lock
similarity index 100%
rename from pkgs/tools/typesetting/kramdown-asciidoc/Gemfile.lock
rename to pkgs/by-name/kr/kramdown-asciidoc/Gemfile.lock
diff --git a/pkgs/tools/typesetting/kramdown-asciidoc/gemset.nix b/pkgs/by-name/kr/kramdown-asciidoc/gemset.nix
similarity index 100%
rename from pkgs/tools/typesetting/kramdown-asciidoc/gemset.nix
rename to pkgs/by-name/kr/kramdown-asciidoc/gemset.nix
diff --git a/pkgs/tools/typesetting/kramdown-asciidoc/default.nix b/pkgs/by-name/kr/kramdown-asciidoc/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/kramdown-asciidoc/default.nix
rename to pkgs/by-name/kr/kramdown-asciidoc/package.nix
diff --git a/pkgs/tools/X11/libstrangle/nixos.patch b/pkgs/by-name/li/libstrangle/nixos.patch
similarity index 100%
rename from pkgs/tools/X11/libstrangle/nixos.patch
rename to pkgs/by-name/li/libstrangle/nixos.patch
diff --git a/pkgs/tools/X11/libstrangle/default.nix b/pkgs/by-name/li/libstrangle/package.nix
similarity index 97%
rename from pkgs/tools/X11/libstrangle/default.nix
rename to pkgs/by-name/li/libstrangle/package.nix
index fb63ed546b228..1a2fb56ea598a 100644
--- a/pkgs/tools/X11/libstrangle/default.nix
+++ b/pkgs/by-name/li/libstrangle/package.nix
@@ -1,13 +1,13 @@
 {
   lib,
-  stdenv,
+  stdenv_32bit,
   fetchFromGitLab,
   fetchpatch,
   libGL,
   libX11,
 }:
 
-stdenv.mkDerivation rec {
+stdenv_32bit.mkDerivation rec {
   pname = "libstrangle";
   version = "unstable-202202022";
 
diff --git a/pkgs/tools/audio/liquidsoap/full.nix b/pkgs/by-name/li/liquidsoap/package.nix
similarity index 97%
rename from pkgs/tools/audio/liquidsoap/full.nix
rename to pkgs/by-name/li/liquidsoap/package.nix
index 52578b24191e1..5eec38b5de54d 100644
--- a/pkgs/tools/audio/liquidsoap/full.nix
+++ b/pkgs/by-name/li/liquidsoap/package.nix
@@ -6,21 +6,24 @@
   which,
   pkg-config,
   libjpeg,
-  ocamlPackages,
+  ocaml-ng,
   awscli2,
   bubblewrap,
   curl,
   dune,
-  ffmpeg,
+  ffmpeg_6-full,
   yt-dlp,
   runtimePackages ? [
     awscli2
     bubblewrap
     curl
-    ffmpeg
+    ffmpeg_6-full
     yt-dlp
   ],
 }:
+let
+  ocamlPackages = ocaml-ng.ocamlPackages_4_14;
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "liquidsoap";
   version = "2.4.2";
diff --git a/pkgs/tools/admin/meraki-cli/default.nix b/pkgs/by-name/me/meraki-cli/package.nix
similarity index 80%
rename from pkgs/tools/admin/meraki-cli/default.nix
rename to pkgs/by-name/me/meraki-cli/package.nix
index 066c5cedffa2e..1080ecfe0ae63 100644
--- a/pkgs/tools/admin/meraki-cli/default.nix
+++ b/pkgs/by-name/me/meraki-cli/package.nix
@@ -1,17 +1,10 @@
 {
   lib,
-  argcomplete,
-  jinja2,
-  meraki,
-  rich,
+  python3Packages,
   fetchPypi,
-  buildPythonApplication,
-  pytestCheckHook,
-  requests-mock,
-  setuptools,
 }:
 
-buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "meraki-cli";
   version = "1.5.1";
   pyproject = true;
@@ -30,18 +23,18 @@ buildPythonApplication rec {
     "TestUpgrade"
   ];
 
-  build-system = [
+  build-system = with python3Packages; [
     setuptools
   ];
 
-  dependencies = [
+  dependencies = with python3Packages; [
     argcomplete
     jinja2
     meraki
     rich
   ];
 
-  nativeCheckInputs = [
+  nativeCheckInputs = with python3Packages; [
     pytestCheckHook
     requests-mock
   ];
diff --git a/pkgs/tools/filesystems/mergerfs/tools.nix b/pkgs/by-name/me/mergerfs-tools/package.nix
similarity index 100%
rename from pkgs/tools/filesystems/mergerfs/tools.nix
rename to pkgs/by-name/me/mergerfs-tools/package.nix
diff --git a/pkgs/tools/filesystems/mergerfs/default.nix b/pkgs/by-name/me/mergerfs/package.nix
similarity index 100%
rename from pkgs/tools/filesystems/mergerfs/default.nix
rename to pkgs/by-name/me/mergerfs/package.nix
diff --git a/pkgs/tools/admin/meshcentral/fix-js-include-paths.patch b/pkgs/by-name/me/meshcentral/fix-js-include-paths.patch
similarity index 100%
rename from pkgs/tools/admin/meshcentral/fix-js-include-paths.patch
rename to pkgs/by-name/me/meshcentral/fix-js-include-paths.patch
diff --git a/pkgs/tools/admin/meshcentral/package.json b/pkgs/by-name/me/meshcentral/package.json
similarity index 100%
rename from pkgs/tools/admin/meshcentral/package.json
rename to pkgs/by-name/me/meshcentral/package.json
diff --git a/pkgs/tools/admin/meshcentral/default.nix b/pkgs/by-name/me/meshcentral/package.nix
similarity index 100%
rename from pkgs/tools/admin/meshcentral/default.nix
rename to pkgs/by-name/me/meshcentral/package.nix
diff --git a/pkgs/tools/admin/meshcentral/update.sh b/pkgs/by-name/me/meshcentral/update.sh
similarity index 100%
rename from pkgs/tools/admin/meshcentral/update.sh
rename to pkgs/by-name/me/meshcentral/update.sh
diff --git a/pkgs/tools/admin/meshcentral/yarn.lock b/pkgs/by-name/me/meshcentral/yarn.lock
similarity index 100%
rename from pkgs/tools/admin/meshcentral/yarn.lock
rename to pkgs/by-name/me/meshcentral/yarn.lock
diff --git a/pkgs/tools/filesystems/mkspiffs/default.nix b/pkgs/by-name/mk/mkspiffs/package.nix
similarity index 100%
rename from pkgs/tools/filesystems/mkspiffs/default.nix
rename to pkgs/by-name/mk/mkspiffs/package.nix
diff --git a/pkgs/tools/filesystems/mkspiffs/presets.nix b/pkgs/by-name/mk/mkspiffs/presets.nix
similarity index 100%
rename from pkgs/tools/filesystems/mkspiffs/presets.nix
rename to pkgs/by-name/mk/mkspiffs/presets.nix
diff --git a/pkgs/tools/games/pokefinder/default.nix b/pkgs/by-name/po/pokefinder/package.nix
similarity index 91%
rename from pkgs/tools/games/pokefinder/default.nix
rename to pkgs/by-name/po/pokefinder/package.nix
index f291d461e23e1..8755f55770f41 100644
--- a/pkgs/tools/games/pokefinder/default.nix
+++ b/pkgs/by-name/po/pokefinder/package.nix
@@ -4,14 +4,10 @@
   copyDesktopItems,
   makeDesktopItem,
   fetchFromGitHub,
-  fetchpatch,
   cmake,
   python3,
-  qtbase,
-  qttools,
-  qtwayland,
+  qt6,
   imagemagick,
-  wrapQtAppsHook,
   gitUpdater,
 }:
 
@@ -53,7 +49,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [
     cmake
-    wrapQtAppsHook
+    qt6.wrapQtAppsHook
     python3
   ]
   ++ lib.optionals (!stdenv.hostPlatform.isDarwin) [
@@ -73,10 +69,10 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    qtbase
-    qttools
+    qt6.qtbase
+    qt6.qttools
   ]
-  ++ lib.optionals stdenv.hostPlatform.isLinux [ qtwayland ];
+  ++ lib.optionals stdenv.hostPlatform.isLinux [ qt6.qtwayland ];
 
   passthru.updateScript = gitUpdater {
     rev-prefix = "v";
diff --git a/pkgs/tools/games/pokefinder/set-desktop-file-name.patch b/pkgs/by-name/po/pokefinder/set-desktop-file-name.patch
similarity index 100%
rename from pkgs/tools/games/pokefinder/set-desktop-file-name.patch
rename to pkgs/by-name/po/pokefinder/set-desktop-file-name.patch
diff --git a/pkgs/tools/admin/pulumi-bin/data.nix b/pkgs/by-name/pu/pulumi-bin/data.nix
similarity index 100%
rename from pkgs/tools/admin/pulumi-bin/data.nix
rename to pkgs/by-name/pu/pulumi-bin/data.nix
diff --git a/pkgs/tools/admin/pulumi-bin/default.nix b/pkgs/by-name/pu/pulumi-bin/package.nix
similarity index 100%
rename from pkgs/tools/admin/pulumi-bin/default.nix
rename to pkgs/by-name/pu/pulumi-bin/package.nix
diff --git a/pkgs/tools/admin/pulumi-bin/update.sh b/pkgs/by-name/pu/pulumi-bin/update.sh
similarity index 98%
rename from pkgs/tools/admin/pulumi-bin/update.sh
rename to pkgs/by-name/pu/pulumi-bin/update.sh
index 16385373a272f..f718121355525 100755
--- a/pkgs/tools/admin/pulumi-bin/update.sh
+++ b/pkgs/by-name/pu/pulumi-bin/update.sh
@@ -1,5 +1,5 @@
 #!/usr/bin/env nix-shell
-#!nix-shell update-pulumi-shell.nix -i bash
+#!nix-shell -i bash -p gh
 # shellcheck shell=bash
 # Bash 3 compatible for Darwin
 
diff --git a/pkgs/tools/backup/pyznap/default.nix b/pkgs/by-name/py/pyznap/package.nix
similarity index 83%
rename from pkgs/tools/backup/pyznap/default.nix
rename to pkgs/by-name/py/pyznap/package.nix
index 082ffe7df651e..54aa459d6b3bb 100644
--- a/pkgs/tools/backup/pyznap/default.nix
+++ b/pkgs/by-name/py/pyznap/package.nix
@@ -1,11 +1,10 @@
 {
   lib,
-  buildPythonApplication,
+  python3Packages,
   fetchPypi,
-  setuptools,
 }:
 
-buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "pyznap";
   version = "1.6.0";
   format = "setuptools";
@@ -15,7 +14,7 @@ buildPythonApplication rec {
     sha256 = "88bf1d6de2c11f14acbdfa01b61eb95c94f95d829ddebdaee3786b64ccb93ae3";
   };
 
-  propagatedBuildInputs = [
+  propagatedBuildInputs = with python3Packages; [
     setuptools
   ];
 
diff --git a/pkgs/tools/virtualization/supermin/default.nix b/pkgs/by-name/su/supermin/package.nix
similarity index 94%
rename from pkgs/tools/virtualization/supermin/default.nix
rename to pkgs/by-name/su/supermin/package.nix
index 6f7692bd97d22..e8f89bc8dc4d6 100644
--- a/pkgs/tools/virtualization/supermin/default.nix
+++ b/pkgs/by-name/su/supermin/package.nix
@@ -6,7 +6,7 @@
   e2fsprogs,
   perl,
   pkg-config,
-  ocamlPackages,
+  ocaml-ng,
   glibc,
 }:
 
@@ -25,7 +25,7 @@ stdenv.mkDerivation (finalAttrs: {
     perl
     pkg-config
   ]
-  ++ (with ocamlPackages; [
+  ++ (with ocaml-ng.ocamlPackages_4_14; [
     findlib
     ocaml
   ]);
diff --git a/pkgs/tools/video/swftools/default.nix b/pkgs/by-name/sw/swftools/package.nix
similarity index 95%
rename from pkgs/tools/video/swftools/default.nix
rename to pkgs/by-name/sw/swftools/package.nix
index 60ab7234fa84a..4f9b6a76d0736 100644
--- a/pkgs/tools/video/swftools/default.nix
+++ b/pkgs/by-name/sw/swftools/package.nix
@@ -1,13 +1,13 @@
 {
   lib,
-  stdenv,
+  gccStdenv,
   fetchurl,
   freetype,
   libjpeg,
   zlib,
 }:
 
-stdenv.mkDerivation rec {
+gccStdenv.mkDerivation rec {
   pname = "swftools";
   version = "0.9.2";
 
diff --git a/pkgs/tools/video/swftools/swftools.patch b/pkgs/by-name/sw/swftools/swftools.patch
similarity index 100%
rename from pkgs/tools/video/swftools/swftools.patch
rename to pkgs/by-name/sw/swftools/swftools.patch
diff --git a/pkgs/tools/audio/tidal-dl/default.nix b/pkgs/by-name/ti/tidal-dl/package.nix
similarity index 81%
rename from pkgs/tools/audio/tidal-dl/default.nix
rename to pkgs/by-name/ti/tidal-dl/package.nix
index 89fb185d793ec..e89e05d6dbae2 100644
--- a/pkgs/tools/audio/tidal-dl/default.nix
+++ b/pkgs/by-name/ti/tidal-dl/package.nix
@@ -1,11 +1,10 @@
 {
   lib,
-  buildPythonApplication,
+  python3Packages,
   fetchPypi,
-  aigpy,
 }:
 
-buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "tidal-dl";
   version = "2022.10.31.1";
   format = "setuptools";
@@ -15,7 +14,7 @@ buildPythonApplication rec {
     hash = "sha256-b2AAsiI3n2/v6HC37fMI/d8UcxZxsWM+fnWvdajHrOg=";
   };
 
-  propagatedBuildInputs = [ aigpy ];
+  propagatedBuildInputs = with python3Packages; [ aigpy ];
 
   meta = {
     homepage = "https://github.com/yaronzz/Tidal-Media-Downloader";
diff --git a/pkgs/tools/typesetting/tikzit/default.nix b/pkgs/by-name/ti/tikzit/package.nix
similarity index 90%
rename from pkgs/tools/typesetting/tikzit/default.nix
rename to pkgs/by-name/ti/tikzit/package.nix
index 481bc29d1d6f7..4531d766617cb 100644
--- a/pkgs/tools/typesetting/tikzit/default.nix
+++ b/pkgs/by-name/ti/tikzit/package.nix
@@ -2,13 +2,10 @@
   lib,
   stdenv,
   fetchFromGitHub,
-  qmake,
-  qttools,
-  qtbase,
-  poppler,
+  qt5,
   flex,
   bison,
-  wrapQtAppsHook,
+  libsForQt5,
 }:
 
 stdenv.mkDerivation {
@@ -23,15 +20,15 @@ stdenv.mkDerivation {
   };
 
   nativeBuildInputs = [
-    qmake
-    qttools
+    qt5.qmake
+    qt5.qttools
     flex
     bison
-    wrapQtAppsHook
+    qt5.wrapQtAppsHook
   ];
   buildInputs = [
-    qtbase
-    poppler
+    qt5.qtbase
+    libsForQt5.poppler
   ];
 
   # src/data/tikzlexer.l:29:10: fatal error: tikzparser.parser.hpp: No such file or directory
diff --git a/pkgs/tools/admin/turbovnc/default.nix b/pkgs/by-name/tu/turbovnc/package.nix
similarity index 98%
rename from pkgs/tools/admin/turbovnc/default.nix
rename to pkgs/by-name/tu/turbovnc/package.nix
index 6d6e7b297ccf4..5b9f6f5810f46 100644
--- a/pkgs/tools/admin/turbovnc/default.nix
+++ b/pkgs/by-name/tu/turbovnc/package.nix
@@ -12,6 +12,7 @@
   libGL,
   libgbm,
   libjpeg_turbo,
+  libjpeg_turbo' ? libjpeg_turbo.override { enableJava = true; },
   makeWrapper,
   mesa-gl-headers, # for built-in 3D software rendering using swrast
   openjdk, # for the client with Java GUI
@@ -84,7 +85,7 @@ stdenv.mkDerivation (finalAttrs: {
     freetype
     libGL # for -DTVNC_SYSTEMX11=1
     libgbm
-    libjpeg_turbo
+    libjpeg_turbo'
     openssl
     pam
     perl
diff --git a/pkgs/tools/backup/ugarit-manifest-maker/eggs.nix b/pkgs/by-name/ug/ugarit-manifest-maker/eggs.nix
similarity index 100%
rename from pkgs/tools/backup/ugarit-manifest-maker/eggs.nix
rename to pkgs/by-name/ug/ugarit-manifest-maker/eggs.nix
diff --git a/pkgs/tools/backup/ugarit-manifest-maker/default.nix b/pkgs/by-name/ug/ugarit-manifest-maker/package.nix
similarity index 77%
rename from pkgs/tools/backup/ugarit-manifest-maker/default.nix
rename to pkgs/by-name/ug/ugarit-manifest-maker/package.nix
index 963a400795d44..2811980c095fb 100644
--- a/pkgs/tools/backup/ugarit-manifest-maker/default.nix
+++ b/pkgs/by-name/ug/ugarit-manifest-maker/package.nix
@@ -1,20 +1,18 @@
 {
-  pkgs,
   lib,
-  eggDerivation,
-  fetchegg,
+  chickenPackages_4,
 }:
 
 let
-  eggs = import ./eggs.nix { inherit eggDerivation fetchegg; };
+  eggs = import ./eggs.nix { inherit (chickenPackages_4) eggDerivation fetchegg; };
 in
 
-eggDerivation rec {
+chickenPackages_4.eggDerivation rec {
   pname = "ugarit-manifest-maker";
   version = "0.1";
   name = "${pname}-${version}";
 
-  src = fetchegg {
+  src = chickenPackages_4.fetchegg {
     inherit version;
     name = pname;
     sha256 = "1jv8lhn4s5a3qphqd3zfwl1py0m5cmqj1h55ys0935m5f422547q";
diff --git a/pkgs/tools/backup/ugarit/eggs.nix b/pkgs/by-name/ug/ugarit/eggs.nix
similarity index 100%
rename from pkgs/tools/backup/ugarit/eggs.nix
rename to pkgs/by-name/ug/ugarit/eggs.nix
diff --git a/pkgs/tools/backup/ugarit/default.nix b/pkgs/by-name/ug/ugarit/package.nix
similarity index 79%
rename from pkgs/tools/backup/ugarit/default.nix
rename to pkgs/by-name/ug/ugarit/package.nix
index 02ea3966d1b99..12504c80de8ee 100644
--- a/pkgs/tools/backup/ugarit/default.nix
+++ b/pkgs/by-name/ug/ugarit/package.nix
@@ -1,20 +1,19 @@
 {
   lib,
-  eggDerivation,
-  fetchegg,
+  chickenPackages_4,
   z3,
 }:
 
 let
-  eggs = import ./eggs.nix { inherit eggDerivation fetchegg; };
+  eggs = import ./eggs.nix { inherit (chickenPackages_4) eggDerivation fetchegg; };
 in
 
-eggDerivation rec {
+chickenPackages_4.eggDerivation rec {
   pname = "ugarit";
   version = "2.0";
   name = "${pname}-${version}";
 
-  src = fetchegg {
+  src = chickenPackages_4.fetchegg {
     inherit version;
     name = pname;
     sha256 = "1l5zkr6b8l5dw9p5mimbva0ncqw1sbvp3d4cywm1hqx2m03a0f1n";
diff --git a/pkgs/tools/backup/ugarit/posix-extras-add-sysmacros-include.patch b/pkgs/by-name/ug/ugarit/posix-extras-add-sysmacros-include.patch
similarity index 100%
rename from pkgs/tools/backup/ugarit/posix-extras-add-sysmacros-include.patch
rename to pkgs/by-name/ug/ugarit/posix-extras-add-sysmacros-include.patch
diff --git a/pkgs/tools/archivers/unar/default.nix b/pkgs/by-name/un/unar/package.nix
similarity index 98%
rename from pkgs/tools/archivers/unar/default.nix
rename to pkgs/by-name/un/unar/package.nix
index 43806054954d8..12b097178bebd 100644
--- a/pkgs/tools/archivers/unar/default.nix
+++ b/pkgs/by-name/un/unar/package.nix
@@ -1,6 +1,6 @@
 {
   lib,
-  stdenv,
+  clangStdenv,
   fetchFromGitHub,
   installShellFiles,
   gnustep-base,
@@ -11,7 +11,9 @@
   wavpack,
   xcbuildHook,
 }:
-
+let
+  stdenv = clangStdenv;
+in
 stdenv.mkDerivation rec {
   pname = "unar";
   version = "1.10.8";
diff --git a/pkgs/tools/cd-dvd/unetbootin/default.nix b/pkgs/by-name/un/unetbootin/package.nix
similarity index 93%
rename from pkgs/tools/cd-dvd/unetbootin/default.nix
rename to pkgs/by-name/un/unetbootin/package.nix
index c51e3b8a9df01..f0179e7ec99ca 100644
--- a/pkgs/tools/cd-dvd/unetbootin/default.nix
+++ b/pkgs/by-name/un/unetbootin/package.nix
@@ -5,10 +5,7 @@
   fetchFromGitHub,
   mtools,
   p7zip,
-  wrapQtAppsHook,
-  qtbase,
-  qttools,
-  qmake,
+  qt5,
   syslinux,
   util-linux,
   which,
@@ -30,12 +27,12 @@ stdenv.mkDerivation rec {
   '';
 
   buildInputs = [
-    qtbase
-    qttools
-    qmake
+    qt5.qtbase
+    qt5.qttools
+    qt5.qmake
   ];
 
-  nativeBuildInputs = [ wrapQtAppsHook ];
+  nativeBuildInputs = [ qt5.wrapQtAppsHook ];
 
   # Lots of nice hard-coded paths...
   postPatch = ''
diff --git a/pkgs/tools/archivers/unrar-wrapper/default.nix b/pkgs/by-name/un/unrar-wrapper/package.nix
similarity index 94%
rename from pkgs/tools/archivers/unrar-wrapper/default.nix
rename to pkgs/by-name/un/unrar-wrapper/package.nix
index a6b697eb2a5d6..f504d181799d3 100644
--- a/pkgs/tools/archivers/unrar-wrapper/default.nix
+++ b/pkgs/by-name/un/unrar-wrapper/package.nix
@@ -1,11 +1,11 @@
 {
   lib,
-  buildPythonApplication,
+  python3Packages,
   fetchFromGitHub,
   unar,
 }:
 
-buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   pname = "unrar-wrapper";
   version = "1.0.0";
   format = "setuptools";
diff --git a/pkgs/tools/archivers/unrar-wrapper/setup-hook.sh b/pkgs/by-name/un/unrar-wrapper/setup-hook.sh
similarity index 100%
rename from pkgs/tools/archivers/unrar-wrapper/setup-hook.sh
rename to pkgs/by-name/un/unrar-wrapper/setup-hook.sh
diff --git a/pkgs/tools/X11/virtualgl/default.nix b/pkgs/by-name/vi/virtualgl/package.nix
similarity index 70%
rename from pkgs/tools/X11/virtualgl/default.nix
rename to pkgs/by-name/vi/virtualgl/package.nix
index 15de52551f3e5..ee8ec969d70a5 100644
--- a/pkgs/tools/X11/virtualgl/default.nix
+++ b/pkgs/by-name/vi/virtualgl/package.nix
@@ -2,10 +2,11 @@
   stdenv,
   lib,
   virtualglLib,
-  virtualglLib_i686 ? null,
+  pkgsi686Linux,
   makeWrapper,
   vulkan-loader,
   addDriverRunpath,
+  usei686VirtualglLib ? stdenv.hostPlatform.system == "x86_64-linux",
 }:
 
 stdenv.mkDerivation {
@@ -25,7 +26,7 @@ stdenv.mkDerivation {
       --prefix LD_LIBRARY_PATH : "${
         lib.makeLibraryPath [
           virtualglLib
-          virtualglLib_i686
+          (if usei686VirtualglLib then pkgsi686Linux.virtualglLib else null) # TODO use lib.optional(s) for this
 
           addDriverRunpath.driverLink
 
@@ -34,8 +35,8 @@ stdenv.mkDerivation {
         ]
       }"
   ''
-  + lib.optionalString (virtualglLib_i686 != null) ''
-    ln -sf ${virtualglLib_i686}/bin/.vglrun.vars32 $out/bin
+  + lib.optionalString usei686VirtualglLib ''
+    ln -sf ${pkgsi686Linux.virtualglLib}/bin/.vglrun.vars32 $out/bin
   '';
 
   meta = {
diff --git a/pkgs/tools/X11/virtualgl/lib.nix b/pkgs/by-name/vi/virtualglLib/package.nix
similarity index 98%
rename from pkgs/tools/X11/virtualgl/lib.nix
rename to pkgs/by-name/vi/virtualglLib/package.nix
index bd4d5e9edf723..3160ac60d939b 100644
--- a/pkgs/tools/X11/virtualgl/lib.nix
+++ b/pkgs/by-name/vi/virtualglLib/package.nix
@@ -9,7 +9,7 @@
   libXtst,
   libXi,
   libjpeg_turbo,
-  fltk,
+  fltk_1_3,
   libxcb-keysyms,
   opencl-headers,
   opencl-clhpp,
@@ -46,7 +46,7 @@ stdenv.mkDerivation rec {
     libjpeg_turbo
     libGL
     libGLU
-    fltk
+    fltk_1_3
     libXv
     libXtst
     libXi
diff --git a/pkgs/tools/admin/winbox/default.nix b/pkgs/by-name/wi/winbox3/package.nix
similarity index 97%
rename from pkgs/tools/admin/winbox/default.nix
rename to pkgs/by-name/wi/winbox3/package.nix
index 752522c436c84..f9687ca6785c8 100644
--- a/pkgs/tools/admin/winbox/default.nix
+++ b/pkgs/by-name/wi/winbox3/package.nix
@@ -5,10 +5,11 @@
   copyDesktopItems,
   makeDesktopItem,
   makeBinaryWrapper,
-  wine,
+  wineWowPackages,
 }:
 
 let
+  wine = wineWowPackages.stable;
   # The icon is also from the winbox AUR package (see above).
   icon = fetchurl {
     name = "winbox.png";
diff --git a/pkgs/tools/X11/xbindkeys-config/.editorconfig b/pkgs/by-name/xb/xbindkeys-config/.editorconfig
similarity index 100%
rename from pkgs/tools/X11/xbindkeys-config/.editorconfig
rename to pkgs/by-name/xb/xbindkeys-config/.editorconfig
diff --git a/pkgs/tools/X11/xbindkeys-config/default.nix b/pkgs/by-name/xb/xbindkeys-config/package.nix
similarity index 99%
rename from pkgs/tools/X11/xbindkeys-config/default.nix
rename to pkgs/by-name/xb/xbindkeys-config/package.nix
index 3a0bb35223cf5..ca61178059b14 100644
--- a/pkgs/tools/X11/xbindkeys-config/default.nix
+++ b/pkgs/by-name/xb/xbindkeys-config/package.nix
@@ -6,7 +6,6 @@
   pkg-config,
   procps,
   makeWrapper,
-  ...
 }:
 
 stdenv.mkDerivation rec {
diff --git a/pkgs/tools/X11/xbindkeys-config/xbindkeys-config-patch1.patch b/pkgs/by-name/xb/xbindkeys-config/xbindkeys-config-patch1.patch
similarity index 100%
rename from pkgs/tools/X11/xbindkeys-config/xbindkeys-config-patch1.patch
rename to pkgs/by-name/xb/xbindkeys-config/xbindkeys-config-patch1.patch
diff --git a/pkgs/tools/X11/xbindkeys-config/xbindkeys-config.1 b/pkgs/by-name/xb/xbindkeys-config/xbindkeys-config.1
similarity index 100%
rename from pkgs/tools/X11/xbindkeys-config/xbindkeys-config.1
rename to pkgs/by-name/xb/xbindkeys-config/xbindkeys-config.1
diff --git a/pkgs/tools/typesetting/xmlto/default.nix b/pkgs/by-name/xm/xmlto/package.nix
similarity index 98%
rename from pkgs/tools/typesetting/xmlto/default.nix
rename to pkgs/by-name/xm/xmlto/package.nix
index b180d4007c452..5afdd332b3cfb 100644
--- a/pkgs/tools/typesetting/xmlto/default.nix
+++ b/pkgs/by-name/xm/xmlto/package.nix
@@ -17,7 +17,7 @@
   makeWrapper,
   stdenv,
   testers,
-  w3m,
+  w3m-batch,
 }:
 
 stdenv.mkDerivation (finalAttrs: {
@@ -68,7 +68,7 @@ stdenv.mkDerivation (finalAttrs: {
            libxslt
            libxml2
            getopt
-           w3m
+           w3m-batch
          ]
        }"
   '';
diff --git a/pkgs/tools/audio/yabridge/hardcode-dependencies.patch b/pkgs/by-name/ya/yabridge/hardcode-dependencies.patch
similarity index 100%
rename from pkgs/tools/audio/yabridge/hardcode-dependencies.patch
rename to pkgs/by-name/ya/yabridge/hardcode-dependencies.patch
diff --git a/pkgs/tools/audio/yabridge/libyabridge-drop-32-bit-support.patch b/pkgs/by-name/ya/yabridge/libyabridge-drop-32-bit-support.patch
similarity index 100%
rename from pkgs/tools/audio/yabridge/libyabridge-drop-32-bit-support.patch
rename to pkgs/by-name/ya/yabridge/libyabridge-drop-32-bit-support.patch
diff --git a/pkgs/tools/audio/yabridge/libyabridge-from-nix-profiles.patch b/pkgs/by-name/ya/yabridge/libyabridge-from-nix-profiles.patch
similarity index 100%
rename from pkgs/tools/audio/yabridge/libyabridge-from-nix-profiles.patch
rename to pkgs/by-name/ya/yabridge/libyabridge-from-nix-profiles.patch
diff --git a/pkgs/tools/audio/yabridge/default.nix b/pkgs/by-name/ya/yabridge/package.nix
similarity index 98%
rename from pkgs/tools/audio/yabridge/default.nix
rename to pkgs/by-name/ya/yabridge/package.nix
index 553712f2222bd..378e2231744ed 100644
--- a/pkgs/tools/audio/yabridge/default.nix
+++ b/pkgs/by-name/ya/yabridge/package.nix
@@ -8,12 +8,14 @@
   meson,
   ninja,
   pkg-config,
-  wine,
+  wineWowPackages,
   libxcb,
   nix-update-script,
 }:
 
 let
+  wine = wineWowPackages.yabridge;
+
   # Derived from subprojects/asio.wrap
   asio = fetchFromGitHub {
     owner = "chriskohlhoff";
diff --git a/pkgs/tools/audio/yabridgectl/chainloader-from-nix-profiles.patch b/pkgs/by-name/ya/yabridgectl/chainloader-from-nix-profiles.patch
similarity index 100%
rename from pkgs/tools/audio/yabridgectl/chainloader-from-nix-profiles.patch
rename to pkgs/by-name/ya/yabridgectl/chainloader-from-nix-profiles.patch
diff --git a/pkgs/tools/audio/yabridgectl/default.nix b/pkgs/by-name/ya/yabridgectl/package.nix
similarity index 94%
rename from pkgs/tools/audio/yabridgectl/default.nix
rename to pkgs/by-name/ya/yabridgectl/package.nix
index aba3c158d6912..53ee5714dc879 100644
--- a/pkgs/tools/audio/yabridgectl/default.nix
+++ b/pkgs/by-name/ya/yabridgectl/package.nix
@@ -3,7 +3,7 @@
   rustPlatform,
   yabridge,
   makeWrapper,
-  wine,
+  wineWowPackages,
 }:
 
 rustPlatform.buildRustPackage {
@@ -31,7 +31,7 @@ rustPlatform.buildRustPackage {
     wrapProgram "$out/bin/yabridgectl" \
       --prefix PATH : ${
         lib.makeBinPath [
-          wine # winedump
+          wineWowPackages.yabridge # winedump
         ]
       }
   '';
diff --git a/pkgs/tools/audio/yabridgectl/remove-dependency-verification.patch b/pkgs/by-name/ya/yabridgectl/remove-dependency-verification.patch
similarity index 100%
rename from pkgs/tools/audio/yabridgectl/remove-dependency-verification.patch
rename to pkgs/by-name/ya/yabridgectl/remove-dependency-verification.patch
diff --git a/pkgs/tools/admin/pulumi-bin/update-pulumi-shell.nix b/pkgs/tools/admin/pulumi-bin/update-pulumi-shell.nix
deleted file mode 100644
index 8101f1b5b926e..0000000000000
--- a/pkgs/tools/admin/pulumi-bin/update-pulumi-shell.nix
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-  nixpkgs ? import ../../../.. { },
-}:
-with nixpkgs;
-mkShell {
-  packages = [
-    pkgs.gh
-  ];
-}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 0acf541c941af..e5bcf8ee3b6cc 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -991,10 +991,6 @@ with pkgs;
 
   dehinter = with python3Packages; toPythonApplication dehinter;
 
-  gamemode = callPackage ../tools/games/gamemode {
-    libgamemode32 = pkgsi686Linux.gamemode.lib;
-  };
-
   gamescope-wsi = callPackage ../by-name/ga/gamescope/package.nix {
     enableExecutable = false;
     enableWsi = true;
@@ -1040,10 +1036,6 @@ with pkgs;
 
   shaperglot = with python3Packages; toPythonApplication shaperglot;
 
-  supermin = callPackage ../tools/virtualization/supermin {
-    ocamlPackages = ocaml-ng.ocamlPackages_4_14;
-  };
-
   ufolint = with python3Packages; toPythonApplication ufolint;
 
   ventoy-full = ventoy.override {
@@ -1066,17 +1058,6 @@ with pkgs;
   waydroid-nftables = waydroid.override { withNftables = true; };
 
   winbox = winbox3;
-  winbox3 = callPackage ../tools/admin/winbox {
-    wine = wineWowPackages.stable;
-  };
-
-  yabridge = callPackage ../tools/audio/yabridge {
-    wine = wineWowPackages.yabridge;
-  };
-
-  yabridgectl = callPackage ../tools/audio/yabridgectl {
-    wine = wineWowPackages.yabridge;
-  };
 
   ### APPLICATIONS/VERSION-MANAGEMENT
 
@@ -1662,8 +1643,6 @@ with pkgs;
 
   clickgen = with python3Packages; toPythonApplication clickgen;
 
-  cloud-init = callPackage ../tools/virtualization/cloud-init { inherit systemd; };
-
   coloredlogs = with python3Packages; toPythonApplication coloredlogs;
 
   czkawka-full = czkawka.wrapper.override {
@@ -1729,10 +1708,6 @@ with pkgs;
     plugins = lib.filter (p: p ? pluginName) (builtins.attrValues discourse.plugins);
   };
 
-  disorderfs = callPackage ../tools/filesystems/disorderfs {
-    asciidoc = asciidoc-full;
-  };
-
   dino = callPackage ../applications/networking/instant-messengers/dino { };
 
   dnschef = python3Packages.callPackage ../tools/networking/dnschef { };
@@ -1907,9 +1882,7 @@ with pkgs;
           throw "mesonEmulatorHook may only be added to nativeBuildInputs when the target binaries can't be executed; however you are attempting to use it in a situation where ${stdenv.hostPlatform.config} can execute ${stdenv.targetPlatform.config}. Consider only adding mesonEmulatorHook according to a conditional based canExecute in your package expression."
       );
 
-  mkspiffs = callPackage ../tools/filesystems/mkspiffs { };
-
-  mkspiffs-presets = recurseIntoAttrs (callPackages ../tools/filesystems/mkspiffs/presets.nix { });
+  mkspiffs-presets = recurseIntoAttrs (callPackages ../by-name/mk/mkspiffs/presets.nix { });
 
   mobilizon = callPackage ../servers/mobilizon {
     beamPackages = beam.packages.erlang_27.extend (self: super: { elixir = self.elixir_1_18; });
@@ -1946,8 +1919,6 @@ with pkgs;
 
   pixcat = with python3Packages; toPythonApplication pixcat;
 
-  pyznap = python3Packages.callPackage ../tools/backup/pyznap { };
-
   psrecord = python3Packages.callPackage ../tools/misc/psrecord { };
 
   remarkable-mouse = python3Packages.callPackage ../applications/misc/remarkable/remarkable-mouse { };
@@ -2007,18 +1978,6 @@ with pkgs;
 
   apc-temp-fetch = with python3.pkgs; callPackage ../tools/networking/apc-temp-fetch { };
 
-  asciidoc = callPackage ../tools/typesetting/asciidoc {
-    inherit (python3.pkgs)
-      pygments
-      matplotlib
-      numpy
-      aafigure
-      recursive-pth-loader
-      ;
-    w3m = w3m-batch;
-    enableStandardFeatures = false;
-  };
-
   asciidoc-full = asciidoc.override {
     enableStandardFeatures = true;
   };
@@ -2059,8 +2018,6 @@ with pkgs;
 
   davix-copy = davix.override { enableThirdPartyCopy = true; };
 
-  cdist = python3Packages.callPackage ../tools/admin/cdist { };
-
   cemu-ti = qt5.callPackage ../applications/science/math/cemu-ti { };
 
   libceph = ceph.lib;
@@ -2329,8 +2286,6 @@ with pkgs;
 
   engauge-digitizer = libsForQt5.callPackage ../applications/science/math/engauge-digitizer { };
 
-  kramdown-asciidoc = callPackage ../tools/typesetting/kramdown-asciidoc { };
-
   rocmPackages = recurseIntoAttrs (callPackage ../development/rocm-modules { });
 
   tsm-client-withGui = callPackage ../by-name/ts/tsm-client/package.nix { enableGui = true; };
@@ -2834,8 +2789,6 @@ with pkgs;
 
   keybase-gui = callPackage ../tools/security/keybase/gui.nix { };
 
-  kio-fuse = libsForQt5.callPackage ../tools/filesystems/kio-fuse { };
-
   krunvm = callPackage ../applications/virtualization/krunvm {
     inherit (darwin) sigtool;
   };
@@ -2848,11 +2801,6 @@ with pkgs;
 
   limine-full = limine.override { enableAll = true; };
 
-  liquidsoap = callPackage ../tools/audio/liquidsoap/full.nix {
-    ffmpeg = ffmpeg_6-full;
-    ocamlPackages = ocaml-ng.ocamlPackages_4_14;
-  };
-
   loganalyzer = libsForQt5.callPackage ../development/tools/loganalyzer { };
 
   logstash7 = callPackage ../tools/misc/logstash/7.x.nix {
@@ -3338,8 +3286,6 @@ with pkgs;
 
   pulumiPackages = recurseIntoAttrs pulumi.pkgs;
 
-  pulumi-bin = callPackage ../tools/admin/pulumi-bin { };
-
   patch = gnupatch;
 
   pcscliteWithPolkit = pcsclite.override {
@@ -3637,8 +3583,6 @@ with pkgs;
 
   tinc = callPackage ../tools/networking/tinc { };
 
-  tikzit = libsForQt5.callPackage ../tools/typesetting/tikzit { };
-
   tinc_pre = callPackage ../tools/networking/tinc/pre.nix { };
 
   tldr-hs = haskellPackages.tldr;
@@ -3682,8 +3626,6 @@ with pkgs;
     withPython = true;
   };
 
-  unetbootin = libsForQt5.callPackage ../tools/cd-dvd/unetbootin { };
-
   unrpa = with python3Packages; toPythonApplication unrpa;
 
   usort = with python3Packages; toPythonApplication usort;
@@ -3743,11 +3685,6 @@ with pkgs;
 
   truecrack-cuda = truecrack.override { cudaSupport = true; };
 
-  turbovnc = callPackage ../tools/admin/turbovnc {
-    # fontDirectories = [ font-adobe-75dpi font-misc-misc font-cursor-misc font-bh-lucidatypewriter-75dpi ];
-    libjpeg_turbo = libjpeg_turbo.override { enableJava = true; };
-  };
-
   unbound-with-systemd = unbound.override {
     withSystemd = true;
   };
@@ -3765,20 +3702,6 @@ with pkgs;
     withRedis = true;
   };
 
-  unrar-wrapper = python3Packages.callPackage ../tools/archivers/unrar-wrapper { };
-
-  ugarit = callPackage ../tools/backup/ugarit {
-    inherit (chickenPackages_4) eggDerivation fetchegg;
-  };
-
-  ugarit-manifest-maker = callPackage ../tools/backup/ugarit-manifest-maker {
-    inherit (chickenPackages_4) eggDerivation fetchegg;
-  };
-
-  unar = callPackage ../tools/archivers/unar {
-    stdenv = clangStdenv;
-  };
-
   unzipNLS = lowPrio (unzip.override { enableNLS = true; });
 
   inherit (callPackages ../servers/varnish { })
@@ -3817,10 +3740,6 @@ with pkgs;
 
   libxfs = xfsprogs.dev;
 
-  xmlto = callPackage ../tools/typesetting/xmlto {
-    w3m = w3m-batch;
-  };
-
   xorriso = libisoburn;
 
   xvfb-run = callPackage ../tools/misc/xvfb-run {
@@ -6064,8 +5983,6 @@ with pkgs;
 
   mavproxy = python3Packages.callPackage ../applications/science/robotics/mavproxy { };
 
-  meraki-cli = python3Packages.callPackage ../tools/admin/meraki-cli { };
-
   python-matter-server =
     with python3Packages;
     toPythonApplication (
@@ -6275,10 +6192,6 @@ with pkgs;
     stdenv = if stdenv.hostPlatform.isDarwin then gccStdenv else stdenv;
   };
 
-  swftools = callPackage ../tools/video/swftools {
-    stdenv = gccStdenv;
-  };
-
   teensyduino = arduino-core.override {
     withGui = true;
     withTeensyduino = true;
@@ -7256,10 +7169,6 @@ with pkgs;
   mbedtls_2 = callPackage ../development/libraries/mbedtls/2.nix { };
   mbedtls = callPackage ../development/libraries/mbedtls/3.nix { };
 
-  mergerfs = callPackage ../tools/filesystems/mergerfs { };
-
-  mergerfs-tools = callPackage ../tools/filesystems/mergerfs/tools.nix { };
-
   simple-dftd3 = callPackage ../development/libraries/science/chemistry/simple-dftd3 { };
 
   tblite = callPackage ../development/libraries/science/chemistry/tblite { };
@@ -10727,8 +10636,6 @@ with pkgs;
 
   mercurialFull = mercurial.override { fullBuild = true; };
 
-  meshcentral = callPackage ../tools/admin/meshcentral { };
-
   michabo = libsForQt5.callPackage ../applications/misc/michabo { };
 
   minitube = libsForQt5.callPackage ../applications/video/minitube { };
@@ -11010,8 +10917,6 @@ with pkgs;
 
   plover = recurseIntoAttrs (libsForQt5.callPackage ../applications/misc/plover { });
 
-  pokefinder = qt6Packages.callPackage ../tools/games/pokefinder { };
-
   pothos = libsForQt5.callPackage ../applications/radio/pothos { };
 
   # perhaps there are better apps for this task? It's how I had configured my previous system.
@@ -11229,10 +11134,6 @@ with pkgs;
 
   myfitnesspal = with python3Packages; toPythonApplication myfitnesspal;
 
-  libstrangle = callPackage ../tools/X11/libstrangle {
-    stdenv = stdenv_32bit;
-  };
-
   lightdm_qt = lightdm.override { withQt5 = true; };
 
   curaengine_stable = callPackage ../applications/misc/curaengine/stable.nix { };
@@ -11578,15 +11479,6 @@ with pkgs;
     }
   );
 
-  virtualglLib = callPackage ../tools/X11/virtualgl/lib.nix {
-    fltk = fltk_1_3;
-  };
-
-  virtualgl = callPackage ../tools/X11/virtualgl {
-    virtualglLib_i686 =
-      if stdenv.hostPlatform.system == "x86_64-linux" then pkgsi686Linux.virtualglLib else null;
-  };
-
   vlc-bin-universal = vlc-bin.override { variant = "universal"; };
 
   libvlc = vlc.override {
@@ -11707,10 +11599,6 @@ with pkgs;
 
   x32edit = callPackage ../applications/audio/midas/x32edit.nix { };
 
-  xbindkeys-config = callPackage ../tools/X11/xbindkeys-config {
-    gtk = gtk2;
-  };
-
   kodiPackages = recurseIntoAttrs (kodi.packages);
 
   kodi = callPackage ../applications/video/kodi {
@@ -12024,8 +11912,6 @@ with pkgs;
 
   freeciv_gtk = freeciv;
 
-  ibmcloud-cli = callPackage ../tools/admin/ibmcloud-cli { stdenv = stdenvNoCC; };
-
   # used as base package for iortcw forks
   iortcw_sp = callPackage ../by-name/io/iortcw/sp.nix { };
 
@@ -13304,8 +13190,6 @@ with pkgs;
 
   swift-corelibs-libdispatch = swiftPackages.Dispatch;
 
-  tidal-dl = python3Packages.callPackage ../tools/audio/tidal-dl { };
-
   duden = python3Packages.toPythonApplication python3Packages.duden;
 
   yaziPlugins = recurseIntoAttrs (callPackage ../by-name/ya/yazi/plugins { });