diff --git a/nixos/doc/manual/installation/changing-config.chapter.md b/nixos/doc/manual/installation/changing-config.chapter.md
index 07a0074d17e7..192696b74171 100644
--- a/nixos/doc/manual/installation/changing-config.chapter.md
+++ b/nixos/doc/manual/installation/changing-config.chapter.md
@@ -5,12 +5,13 @@ configuration of your machine. Whenever you've [changed
 something](#ch-configuration) in that file, you should do
 
 ```ShellSession
-# nixos-rebuild switch
+$ nixos-rebuild switch --use-remote-sudo
 ```
 
-to build the new configuration, make it the default configuration for
-booting, and try to realise the configuration in the running system
-(e.g., by restarting system services).
+to build the new configuration as your current user, and as the root user,
+make it the default configuration for booting. `switch` will also try to
+realise the configuration in the running system (e.g., by restarting system
+services).
 
 ::: {.warning}
 This command doesn't start/stop [user services](#opt-systemd.user.services)
@@ -19,14 +20,23 @@ user services.
 :::
 
 ::: {.warning}
-These commands must be executed as root, so you should either run them
-from a root shell or by prefixing them with `sudo -i`.
+Applying a configuration is an action that must be done by the root user, so the
+`switch`, `boot` and `test` commands should be ran with the `--use-remote-sudo`
+flag. Despite its odd name, this flag runs the activation script with elevated
+permissions, regardless of whether or not the target system is remote, without
+affecting the other stages of the `nixos-rebuild` call. This allows unprivileged
+users to rebuild the system and only elevate their permissions when necessary.
+
+Alternatively, one can run the whole command as root while preserving user
+environment variables by prefixing the command with `sudo -E`. However, this
+method may create root-owned files in `$HOME/.cache` if Nix decides to use the
+cache during evaluation.
 :::
 
 You can also do
 
 ```ShellSession
-# nixos-rebuild test
+$ nixos-rebuild test --use-remote-sudo
 ```
 
 to build the configuration and switch the running system to it, but
@@ -37,7 +47,7 @@ configuration.
 There is also
 
 ```ShellSession
-# nixos-rebuild boot
+$ nixos-rebuild boot --use-remote-sudo
 ```
 
 to build the configuration and make it the boot default, but not switch
@@ -47,7 +57,7 @@ You can make your configuration show up in a different submenu of the
 GRUB 2 boot screen by giving it a different *profile name*, e.g.
 
 ```ShellSession
-# nixos-rebuild switch -p test
+$ nixos-rebuild switch -p test --use-remote-sudo
 ```
 
 which causes the new configuration (and previous ones created using
@@ -58,7 +68,7 @@ configurations.
 A repl, or read-eval-print loop, is also available. You can inspect your configuration and use the Nix language with
 
 ```ShellSession
-# nixos-rebuild repl
+$ nixos-rebuild repl
 ```
 
 Your configuration is loaded into the `config` variable. Use tab for autocompletion, use the `:r` command to reload the configuration files. See `:?` or [`nix repl` in the Nix manual](https://nixos.org/manual/nix/stable/command-ref/new-cli/nix3-repl.html) to learn more.
diff --git a/pkgs/applications/editors/emacs/default.nix b/pkgs/applications/editors/emacs/default.nix
index 8181b69d335d..c65961b275d6 100644
--- a/pkgs/applications/editors/emacs/default.nix
+++ b/pkgs/applications/editors/emacs/default.nix
@@ -2,11 +2,8 @@
 
 lib.makeScope pkgs.newScope (self:
   let
-    gconf = pkgs.gnome2.GConf;
     inherit (self) callPackage;
     inheritedArgs = {
-      inherit gconf;
-
       inherit (pkgs.darwin) sigtool;
       inherit (pkgs.darwin.apple_sdk.frameworks)
         Accelerate AppKit Carbon Cocoa GSS ImageCaptureCore ImageIO IOKit OSAKit
diff --git a/pkgs/applications/editors/emacs/make-emacs.nix b/pkgs/applications/editors/emacs/make-emacs.nix
index f995b073d377..ad77abc0c44f 100644
--- a/pkgs/applications/editors/emacs/make-emacs.nix
+++ b/pkgs/applications/editors/emacs/make-emacs.nix
@@ -16,7 +16,6 @@
 , dbus
 , emacsPackagesFor
 , fetchpatch
-, gconf
 , gettext
 , giflib
 , glib-networking
@@ -73,7 +72,6 @@
 , withDbus ? stdenv.isLinux
 , withGTK2 ? false
 , withGTK3 ? withPgtk && !noGui
-, withGconf ? false
 , withGlibNetworking ? withPgtk || withGTK3 || (withX && withXwidgets)
 , withGpm ? stdenv.isLinux
 , withImageMagick ? lib.versionOlder version "27" && (withX || withNS)
@@ -126,7 +124,6 @@ assert withAcl -> stdenv.isLinux;
 assert withAlsaLib -> stdenv.isLinux;
 assert withGTK2 -> !(withGTK3 || withPgtk);
 assert withGTK3 -> !withGTK2 || withPgtk;
-assert withGconf -> withX;
 assert withGpm -> stdenv.isLinux;
 assert withNS -> stdenv.isDarwin && !(withX || variant == "macport");
 assert withPgtk -> withGTK3 && !withX;
@@ -224,8 +221,6 @@ mkDerivation (finalAttrs: {
     jansson
     libxml2
     ncurses
-  ] ++ lib.optionals withGconf [
-    gconf
   ] ++ lib.optionals withAcl [
     acl
   ] ++ lib.optionals withAlsaLib [
diff --git a/pkgs/applications/terminal-emulators/terminator/default.nix b/pkgs/applications/terminal-emulators/terminator/default.nix
index aedbb761a8ca..01047f26bc63 100644
--- a/pkgs/applications/terminal-emulators/terminator/default.nix
+++ b/pkgs/applications/terminal-emulators/terminator/default.nix
@@ -30,7 +30,6 @@ python3.pkgs.buildPythonApplication rec {
     gobject-introspection
     makeBinaryWrapper
     wrapGAppsHook3
-    python3.pkgs.pytest-runner
   ];
 
   buildInputs = [
diff --git a/pkgs/applications/version-management/gh/default.nix b/pkgs/applications/version-management/gh/default.nix
index 9553872acef4..ef040a4df68f 100644
--- a/pkgs/applications/version-management/gh/default.nix
+++ b/pkgs/applications/version-management/gh/default.nix
@@ -2,16 +2,16 @@
 
 buildGoModule rec {
   pname = "gh";
-  version = "2.56.0";
+  version = "2.57.0";
 
   src = fetchFromGitHub {
     owner = "cli";
     repo = "cli";
     rev = "v${version}";
-    hash = "sha256-PDw2u+2hMiPmQe1lnJXnZk8JVsti/j7Nq5Uv3b7RIk4=";
+    hash = "sha256-HNr/HBt1EqbV+/dLCztucmeAqw3jLPOgQ0WLPxGDYgY=";
   };
 
-  vendorHash = "sha256-rMJWUm79/wBBdVvNdIQc7jqzxfDXphBvGYU3wD/BITk=";
+  vendorHash = "sha256-gPUEfdS4iEzMQGdUNKMmEGRug66NVcrV3zvmkoEsNGo=";
 
   nativeBuildInputs = [ installShellFiles ];
 
diff --git a/pkgs/games/0verkill/default.nix b/pkgs/by-name/_0/_0verkill/package.nix
similarity index 100%
rename from pkgs/games/0verkill/default.nix
rename to pkgs/by-name/_0/_0verkill/package.nix
diff --git a/pkgs/tools/misc/0x/Cargo.lock b/pkgs/by-name/_0/_0x/Cargo.lock
similarity index 100%
rename from pkgs/tools/misc/0x/Cargo.lock
rename to pkgs/by-name/_0/_0x/Cargo.lock
diff --git a/pkgs/tools/misc/0x/default.nix b/pkgs/by-name/_0/_0x/package.nix
similarity index 100%
rename from pkgs/tools/misc/0x/default.nix
rename to pkgs/by-name/_0/_0x/package.nix
diff --git a/pkgs/games/1oom/default.nix b/pkgs/by-name/_1/_1oom/package.nix
similarity index 100%
rename from pkgs/games/1oom/default.nix
rename to pkgs/by-name/_1/_1oom/package.nix
diff --git a/pkgs/applications/science/math/4ti2/default.nix b/pkgs/by-name/_4/_4ti2/package.nix
similarity index 100%
rename from pkgs/applications/science/math/4ti2/default.nix
rename to pkgs/by-name/_4/_4ti2/package.nix
diff --git a/pkgs/applications/misc/9menu/default.nix b/pkgs/by-name/_9/_9menu/package.nix
similarity index 100%
rename from pkgs/applications/misc/9menu/default.nix
rename to pkgs/by-name/_9/_9menu/package.nix
diff --git a/pkgs/tools/graphics/aaphoto/default.nix b/pkgs/by-name/aa/aaphoto/package.nix
similarity index 100%
rename from pkgs/tools/graphics/aaphoto/default.nix
rename to pkgs/by-name/aa/aaphoto/package.nix
diff --git a/pkgs/games/ace-of-penguins/fixup-miscompilations.patch b/pkgs/by-name/ac/ace-of-penguins/fixup-miscompilations.patch
similarity index 100%
rename from pkgs/games/ace-of-penguins/fixup-miscompilations.patch
rename to pkgs/by-name/ac/ace-of-penguins/fixup-miscompilations.patch
diff --git a/pkgs/games/ace-of-penguins/default.nix b/pkgs/by-name/ac/ace-of-penguins/package.nix
similarity index 100%
rename from pkgs/games/ace-of-penguins/default.nix
rename to pkgs/by-name/ac/ace-of-penguins/package.nix
diff --git a/pkgs/development/tools/misc/acr/default.nix b/pkgs/by-name/ac/acr/package.nix
similarity index 100%
rename from pkgs/development/tools/misc/acr/default.nix
rename to pkgs/by-name/ac/acr/package.nix
diff --git a/pkgs/applications/science/geometry/antiprism/default.nix b/pkgs/by-name/an/antiprism/package.nix
similarity index 100%
rename from pkgs/applications/science/geometry/antiprism/default.nix
rename to pkgs/by-name/an/antiprism/package.nix
diff --git a/pkgs/development/tools/misc/argbash/default.nix b/pkgs/by-name/ar/argbash/package.nix
similarity index 100%
rename from pkgs/development/tools/misc/argbash/default.nix
rename to pkgs/by-name/ar/argbash/package.nix
diff --git a/pkgs/development/compilers/as31/0000-getline-break.patch b/pkgs/by-name/as/as31/0000-getline-break.patch
similarity index 100%
rename from pkgs/development/compilers/as31/0000-getline-break.patch
rename to pkgs/by-name/as/as31/0000-getline-break.patch
diff --git a/pkgs/development/compilers/as31/default.nix b/pkgs/by-name/as/as31/package.nix
similarity index 100%
rename from pkgs/development/compilers/as31/default.nix
rename to pkgs/by-name/as/as31/package.nix
diff --git a/pkgs/development/compilers/asl/Makefile-nixos.def b/pkgs/by-name/as/asl/Makefile-nixos.def
similarity index 100%
rename from pkgs/development/compilers/asl/Makefile-nixos.def
rename to pkgs/by-name/as/asl/Makefile-nixos.def
diff --git a/pkgs/development/compilers/asl/default.nix b/pkgs/by-name/as/asl/package.nix
similarity index 100%
rename from pkgs/development/compilers/asl/default.nix
rename to pkgs/by-name/as/asl/package.nix
diff --git a/pkgs/development/compilers/atasm/0000-file-not-found.diff b/pkgs/by-name/at/atasm/0000-file-not-found.diff
similarity index 100%
rename from pkgs/development/compilers/atasm/0000-file-not-found.diff
rename to pkgs/by-name/at/atasm/0000-file-not-found.diff
diff --git a/pkgs/development/compilers/atasm/0001-select-flags.diff b/pkgs/by-name/at/atasm/0001-select-flags.diff
similarity index 100%
rename from pkgs/development/compilers/atasm/0001-select-flags.diff
rename to pkgs/by-name/at/atasm/0001-select-flags.diff
diff --git a/pkgs/development/compilers/atasm/default.nix b/pkgs/by-name/at/atasm/package.nix
similarity index 100%
rename from pkgs/development/compilers/atasm/default.nix
rename to pkgs/by-name/at/atasm/package.nix
diff --git a/pkgs/os-specific/linux/audit/default.nix b/pkgs/by-name/au/audit/package.nix
similarity index 100%
rename from pkgs/os-specific/linux/audit/default.nix
rename to pkgs/by-name/au/audit/package.nix
diff --git a/pkgs/development/libraries/basu/default.nix b/pkgs/by-name/ba/basu/package.nix
similarity index 100%
rename from pkgs/development/libraries/basu/default.nix
rename to pkgs/by-name/ba/basu/package.nix
diff --git a/pkgs/development/libraries/biblesync/default.nix b/pkgs/by-name/bi/biblesync/package.nix
similarity index 100%
rename from pkgs/development/libraries/biblesync/default.nix
rename to pkgs/by-name/bi/biblesync/package.nix
diff --git a/pkgs/games/brogue-ce/default.nix b/pkgs/by-name/br/brogue-ce/package.nix
similarity index 100%
rename from pkgs/games/brogue-ce/default.nix
rename to pkgs/by-name/br/brogue-ce/package.nix
diff --git a/pkgs/games/brogue/default.nix b/pkgs/by-name/br/brogue/package.nix
similarity index 100%
rename from pkgs/games/brogue/default.nix
rename to pkgs/by-name/br/brogue/package.nix
diff --git a/pkgs/development/tools/parsing/byacc/default.nix b/pkgs/by-name/by/byacc/package.nix
similarity index 100%
rename from pkgs/development/tools/parsing/byacc/default.nix
rename to pkgs/by-name/by/byacc/package.nix
diff --git a/pkgs/applications/misc/calcoo/default.nix b/pkgs/by-name/ca/calcoo/package.nix
similarity index 100%
rename from pkgs/applications/misc/calcoo/default.nix
rename to pkgs/by-name/ca/calcoo/package.nix
diff --git a/pkgs/tools/networking/cbftp/default.nix b/pkgs/by-name/cb/cbftp/package.nix
similarity index 100%
rename from pkgs/tools/networking/cbftp/default.nix
rename to pkgs/by-name/cb/cbftp/package.nix
diff --git a/pkgs/development/compilers/cc65/default.nix b/pkgs/by-name/cc/cc65/package.nix
similarity index 100%
rename from pkgs/development/compilers/cc65/default.nix
rename to pkgs/by-name/cc/cc65/package.nix
diff --git a/pkgs/development/libraries/cereal/1.3.0.nix b/pkgs/by-name/ce/cereal_1_3_0/package.nix
similarity index 100%
rename from pkgs/development/libraries/cereal/1.3.0.nix
rename to pkgs/by-name/ce/cereal_1_3_0/package.nix
diff --git a/pkgs/development/libraries/cereal/1.3.2.nix b/pkgs/by-name/ce/cereal_1_3_2/package.nix
similarity index 100%
rename from pkgs/development/libraries/cereal/1.3.2.nix
rename to pkgs/by-name/ce/cereal_1_3_2/package.nix
diff --git a/pkgs/development/libraries/cgreen/default.nix b/pkgs/by-name/cg/cgreen/package.nix
similarity index 100%
rename from pkgs/development/libraries/cgreen/default.nix
rename to pkgs/by-name/cg/cgreen/package.nix
diff --git a/pkgs/applications/science/chemistry/chemtool/default.nix b/pkgs/by-name/ch/chemtool/package.nix
similarity index 100%
rename from pkgs/applications/science/chemistry/chemtool/default.nix
rename to pkgs/by-name/ch/chemtool/package.nix
diff --git a/pkgs/games/chromium-bsu/default.nix b/pkgs/by-name/ch/chromium-bsu/package.nix
similarity index 100%
rename from pkgs/games/chromium-bsu/default.nix
rename to pkgs/by-name/ch/chromium-bsu/package.nix
diff --git a/pkgs/applications/misc/cmatrix/default.nix b/pkgs/by-name/cm/cmatrix/package.nix
similarity index 100%
rename from pkgs/applications/misc/cmatrix/default.nix
rename to pkgs/by-name/cm/cmatrix/package.nix
diff --git a/pkgs/data/fonts/comic-neue/default.nix b/pkgs/by-name/co/comic-neue/package.nix
similarity index 100%
rename from pkgs/data/fonts/comic-neue/default.nix
rename to pkgs/by-name/co/comic-neue/package.nix
diff --git a/pkgs/tools/cd-dvd/cue2pops/default.nix b/pkgs/by-name/cu/cue2pops/package.nix
similarity index 100%
rename from pkgs/tools/cd-dvd/cue2pops/default.nix
rename to pkgs/by-name/cu/cue2pops/package.nix
diff --git a/pkgs/applications/science/math/dap/default.nix b/pkgs/by-name/da/dap/package.nix
similarity index 100%
rename from pkgs/applications/science/math/dap/default.nix
rename to pkgs/by-name/da/dap/package.nix
diff --git a/pkgs/applications/emulators/desmume/default.nix b/pkgs/by-name/de/desmume/package.nix
similarity index 100%
rename from pkgs/applications/emulators/desmume/default.nix
rename to pkgs/by-name/de/desmume/package.nix
diff --git a/pkgs/development/compilers/dev86/default.nix b/pkgs/by-name/de/dev86/package.nix
similarity index 100%
rename from pkgs/development/compilers/dev86/default.nix
rename to pkgs/by-name/de/dev86/package.nix
diff --git a/pkgs/applications/emulators/dgen-sdl/default.nix b/pkgs/by-name/dg/dgen-sdl/package.nix
similarity index 100%
rename from pkgs/applications/emulators/dgen-sdl/default.nix
rename to pkgs/by-name/dg/dgen-sdl/package.nix
diff --git a/pkgs/applications/video/dvdstyler/default.nix b/pkgs/by-name/dv/dvdstyler/package.nix
similarity index 100%
rename from pkgs/applications/video/dvdstyler/default.nix
rename to pkgs/by-name/dv/dvdstyler/package.nix
diff --git a/pkgs/development/compilers/xa/dxa.nix b/pkgs/by-name/dx/dxa/package.nix
similarity index 100%
rename from pkgs/development/compilers/xa/dxa.nix
rename to pkgs/by-name/dx/dxa/package.nix
diff --git a/pkgs/applications/editors/edit/default.nix b/pkgs/by-name/ed/edit/package.nix
similarity index 100%
rename from pkgs/applications/editors/edit/default.nix
rename to pkgs/by-name/ed/edit/package.nix
diff --git a/pkgs/applications/editors/edlin/default.nix b/pkgs/by-name/ed/edlin/package.nix
similarity index 100%
rename from pkgs/applications/editors/edlin/default.nix
rename to pkgs/by-name/ed/edlin/package.nix
diff --git a/pkgs/by-name/ef/efibootmgr/package.nix b/pkgs/by-name/ef/efibootmgr/package.nix
index c81f5123c67a..f53ea4a6abf5 100644
--- a/pkgs/by-name/ef/efibootmgr/package.nix
+++ b/pkgs/by-name/ef/efibootmgr/package.nix
@@ -2,19 +2,26 @@
   lib,
   stdenv,
   fetchFromGitHub,
-  pkg-config,
   efivar,
+  nix-update-script,
+  pkg-config,
   popt,
+  testers,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "efibootmgr";
   version = "18";
 
+  outputs = [
+    "out"
+    "man"
+  ];
+
   src = fetchFromGitHub {
     owner = "rhboot";
     repo = "efibootmgr";
-    rev = version;
+    rev = finalAttrs.version;
     hash = "sha256-DYYQGALEn2+mRHgqCJsA7OQCF7xirIgQlWexZ9uoKcg=";
   };
 
@@ -32,12 +39,18 @@ stdenv.mkDerivation rec {
 
   installFlags = [ "prefix=${placeholder "out"}" ];
 
+  passthru = {
+    tests.version = testers.testVersion { package = finalAttrs.finalPackage; };
+    updateScript = nix-update-script { };
+  };
+
   meta = {
     description = "Linux user-space application to modify the Intel Extensible Firmware Interface (EFI) Boot Manager";
     homepage = "https://github.com/rhboot/efibootmgr";
-    changelog = "https://github.com/rhboot/efibootmgr/releases/tag/${src.rev}";
+    changelog = "https://github.com/rhboot/efibootmgr/releases/tag/${finalAttrs.version}";
     license = lib.licenses.gpl2Only;
     maintainers = with lib.maintainers; [ getchoo ];
+    mainProgram = "efibootmgr";
     platforms = lib.platforms.linux;
   };
-}
+})
diff --git a/pkgs/applications/editors/em/default.nix b/pkgs/by-name/em/em/package.nix
similarity index 100%
rename from pkgs/applications/editors/em/default.nix
rename to pkgs/by-name/em/em/package.nix
diff --git a/pkgs/applications/emulators/emu2/default.nix b/pkgs/by-name/em/emu2/package.nix
similarity index 100%
rename from pkgs/applications/emulators/emu2/default.nix
rename to pkgs/by-name/em/emu2/package.nix
diff --git a/pkgs/development/tools/literate-programming/eweb/default.nix b/pkgs/by-name/ew/eweb/package.nix
similarity index 100%
rename from pkgs/development/tools/literate-programming/eweb/default.nix
rename to pkgs/by-name/ew/eweb/package.nix
diff --git a/pkgs/tools/graphics/flam3/default.nix b/pkgs/by-name/fl/flam3/package.nix
similarity index 100%
rename from pkgs/tools/graphics/flam3/default.nix
rename to pkgs/by-name/fl/flam3/package.nix
diff --git a/pkgs/applications/window-managers/fluxbox/default.nix b/pkgs/by-name/fl/fluxbox/package.nix
similarity index 100%
rename from pkgs/applications/window-managers/fluxbox/default.nix
rename to pkgs/by-name/fl/fluxbox/package.nix
diff --git a/pkgs/applications/graphics/fondo/default.nix b/pkgs/by-name/fo/fondo/package.nix
similarity index 100%
rename from pkgs/applications/graphics/fondo/default.nix
rename to pkgs/by-name/fo/fondo/package.nix
diff --git a/pkgs/development/libraries/ftgl/default.nix b/pkgs/by-name/ft/ftgl/package.nix
similarity index 100%
rename from pkgs/development/libraries/ftgl/default.nix
rename to pkgs/by-name/ft/ftgl/package.nix
diff --git a/pkgs/development/tools/literate-programming/funnelweb/default.nix b/pkgs/by-name/fu/funnelweb/package.nix
similarity index 100%
rename from pkgs/development/tools/literate-programming/funnelweb/default.nix
rename to pkgs/by-name/fu/funnelweb/package.nix
diff --git a/pkgs/tools/misc/gavin-bc/default.nix b/pkgs/by-name/ga/gavin-bc/package.nix
similarity index 100%
rename from pkgs/tools/misc/gavin-bc/default.nix
rename to pkgs/by-name/ga/gavin-bc/package.nix
diff --git a/pkgs/tools/misc/gay/default.nix b/pkgs/by-name/ga/gay/package.nix
similarity index 100%
rename from pkgs/tools/misc/gay/default.nix
rename to pkgs/by-name/ga/gay/package.nix
diff --git a/pkgs/development/libraries/glpng/default.nix b/pkgs/by-name/gl/glpng/package.nix
similarity index 100%
rename from pkgs/development/libraries/glpng/default.nix
rename to pkgs/by-name/gl/glpng/package.nix
diff --git a/pkgs/development/compilers/gnu-smalltalk/0000-fix_mkorder.patch b/pkgs/by-name/gn/gnu-smalltalk/0000-fix_mkorder.patch
similarity index 100%
rename from pkgs/development/compilers/gnu-smalltalk/0000-fix_mkorder.patch
rename to pkgs/by-name/gn/gnu-smalltalk/0000-fix_mkorder.patch
diff --git a/pkgs/development/compilers/gnu-smalltalk/default.nix b/pkgs/by-name/gn/gnu-smalltalk/package.nix
similarity index 100%
rename from pkgs/development/compilers/gnu-smalltalk/default.nix
rename to pkgs/by-name/gn/gnu-smalltalk/package.nix
diff --git a/pkgs/applications/office/gnucash/0001-disable-date-and-time-tests.patch b/pkgs/by-name/gn/gnucash/0001-disable-date-and-time-tests.patch
similarity index 100%
rename from pkgs/applications/office/gnucash/0001-disable-date-and-time-tests.patch
rename to pkgs/by-name/gn/gnucash/0001-disable-date-and-time-tests.patch
diff --git a/pkgs/applications/office/gnucash/0002-disable-gnc-fq-update.patch b/pkgs/by-name/gn/gnucash/0002-disable-gnc-fq-update.patch
similarity index 100%
rename from pkgs/applications/office/gnucash/0002-disable-gnc-fq-update.patch
rename to pkgs/by-name/gn/gnucash/0002-disable-gnc-fq-update.patch
diff --git a/pkgs/applications/office/gnucash/0003-remove-valgrind.patch b/pkgs/by-name/gn/gnucash/0003-remove-valgrind.patch
similarity index 100%
rename from pkgs/applications/office/gnucash/0003-remove-valgrind.patch
rename to pkgs/by-name/gn/gnucash/0003-remove-valgrind.patch
diff --git a/pkgs/applications/office/gnucash/0004-exec-fq-wrapper.patch b/pkgs/by-name/gn/gnucash/0004-exec-fq-wrapper.patch
similarity index 100%
rename from pkgs/applications/office/gnucash/0004-exec-fq-wrapper.patch
rename to pkgs/by-name/gn/gnucash/0004-exec-fq-wrapper.patch
diff --git a/pkgs/applications/office/gnucash/0005-disable-test-lots.patch b/pkgs/by-name/gn/gnucash/0005-disable-test-lots.patch
similarity index 100%
rename from pkgs/applications/office/gnucash/0005-disable-test-lots.patch
rename to pkgs/by-name/gn/gnucash/0005-disable-test-lots.patch
diff --git a/pkgs/applications/office/gnucash/default.nix b/pkgs/by-name/gn/gnucash/package.nix
similarity index 100%
rename from pkgs/applications/office/gnucash/default.nix
rename to pkgs/by-name/gn/gnucash/package.nix
diff --git a/pkgs/applications/office/gnucash/update.sh b/pkgs/by-name/gn/gnucash/update.sh
similarity index 100%
rename from pkgs/applications/office/gnucash/update.sh
rename to pkgs/by-name/gn/gnucash/update.sh
diff --git a/pkgs/servers/gopher/gofish/default.nix b/pkgs/by-name/go/gofish/package.nix
similarity index 100%
rename from pkgs/servers/gopher/gofish/default.nix
rename to pkgs/by-name/go/gofish/package.nix
diff --git a/pkgs/applications/graphics/grafx2/default.nix b/pkgs/by-name/gr/grafx2/package.nix
similarity index 100%
rename from pkgs/applications/graphics/grafx2/default.nix
rename to pkgs/by-name/gr/grafx2/package.nix
diff --git a/pkgs/applications/emulators/gxemul/0001-fix-attributes.patch b/pkgs/by-name/gx/gxemul/0001-fix-attributes.patch
similarity index 100%
rename from pkgs/applications/emulators/gxemul/0001-fix-attributes.patch
rename to pkgs/by-name/gx/gxemul/0001-fix-attributes.patch
diff --git a/pkgs/applications/emulators/gxemul/default.nix b/pkgs/by-name/gx/gxemul/package.nix
similarity index 100%
rename from pkgs/applications/emulators/gxemul/default.nix
rename to pkgs/by-name/gx/gxemul/package.nix
diff --git a/pkgs/applications/window-managers/hackedbox/default.nix b/pkgs/by-name/ha/hackedbox/package.nix
similarity index 100%
rename from pkgs/applications/window-managers/hackedbox/default.nix
rename to pkgs/by-name/ha/hackedbox/package.nix
diff --git a/pkgs/development/libraries/hax11/default.nix b/pkgs/by-name/ha/hax11/package.nix
similarity index 100%
rename from pkgs/development/libraries/hax11/default.nix
rename to pkgs/by-name/ha/hax11/package.nix
diff --git a/pkgs/development/compilers/intercal/default.nix b/pkgs/by-name/in/intercal/package.nix
similarity index 100%
rename from pkgs/development/compilers/intercal/default.nix
rename to pkgs/by-name/in/intercal/package.nix
diff --git a/pkgs/development/interpreters/j/fix-install-path.patch b/pkgs/by-name/j/j/fix-install-path.patch
similarity index 100%
rename from pkgs/development/interpreters/j/fix-install-path.patch
rename to pkgs/by-name/j/j/fix-install-path.patch
diff --git a/pkgs/development/interpreters/j/default.nix b/pkgs/by-name/j/j/package.nix
similarity index 100%
rename from pkgs/development/interpreters/j/default.nix
rename to pkgs/by-name/j/j/package.nix
diff --git a/pkgs/applications/editors/joe/default.nix b/pkgs/by-name/jo/joe/package.nix
similarity index 100%
rename from pkgs/applications/editors/joe/default.nix
rename to pkgs/by-name/jo/joe/package.nix
diff --git a/pkgs/applications/editors/jove/default.nix b/pkgs/by-name/jo/jove/package.nix
similarity index 100%
rename from pkgs/applications/editors/jove/default.nix
rename to pkgs/by-name/jo/jove/package.nix
diff --git a/pkgs/applications/editors/jupp/default.nix b/pkgs/by-name/ju/jupp/package.nix
similarity index 100%
rename from pkgs/applications/editors/jupp/default.nix
rename to pkgs/by-name/ju/jupp/package.nix
diff --git a/pkgs/applications/networking/irc/kirc/default.nix b/pkgs/by-name/ki/kirc/package.nix
similarity index 100%
rename from pkgs/applications/networking/irc/kirc/default.nix
rename to pkgs/by-name/ki/kirc/package.nix
diff --git a/pkgs/applications/misc/lavalauncher/default.nix b/pkgs/by-name/la/lavalauncher/package.nix
similarity index 100%
rename from pkgs/applications/misc/lavalauncher/default.nix
rename to pkgs/by-name/la/lavalauncher/package.nix
diff --git a/pkgs/development/libraries/libarchive/default.nix b/pkgs/by-name/li/libarchive/package.nix
similarity index 100%
rename from pkgs/development/libraries/libarchive/default.nix
rename to pkgs/by-name/li/libarchive/package.nix
diff --git a/pkgs/development/libraries/libast/default.nix b/pkgs/by-name/li/libast/package.nix
similarity index 100%
rename from pkgs/development/libraries/libast/default.nix
rename to pkgs/by-name/li/libast/package.nix
diff --git a/pkgs/development/libraries/libcaca/default.nix b/pkgs/by-name/li/libcaca/package.nix
similarity index 100%
rename from pkgs/development/libraries/libcaca/default.nix
rename to pkgs/by-name/li/libcaca/package.nix
diff --git a/pkgs/development/libraries/libnbd/libnbd-metadata b/pkgs/by-name/li/libnbd/libnbd-metadata
similarity index 100%
rename from pkgs/development/libraries/libnbd/libnbd-metadata
rename to pkgs/by-name/li/libnbd/libnbd-metadata
diff --git a/pkgs/development/libraries/libnbd/default.nix b/pkgs/by-name/li/libnbd/package.nix
similarity index 100%
rename from pkgs/development/libraries/libnbd/default.nix
rename to pkgs/by-name/li/libnbd/package.nix
diff --git a/pkgs/development/libraries/librep/default.nix b/pkgs/by-name/li/librep/package.nix
similarity index 100%
rename from pkgs/development/libraries/librep/default.nix
rename to pkgs/by-name/li/librep/package.nix
diff --git a/pkgs/development/libraries/librep/setup-hook.sh b/pkgs/by-name/li/librep/setup-hook.sh
similarity index 100%
rename from pkgs/development/libraries/librep/setup-hook.sh
rename to pkgs/by-name/li/librep/setup-hook.sh
diff --git a/pkgs/development/libraries/libtap/default.nix b/pkgs/by-name/li/libtap/package.nix
similarity index 100%
rename from pkgs/development/libraries/libtap/default.nix
rename to pkgs/by-name/li/libtap/package.nix
diff --git a/pkgs/development/libraries/libtcod/default.nix b/pkgs/by-name/li/libtcod/package.nix
similarity index 100%
rename from pkgs/development/libraries/libtcod/default.nix
rename to pkgs/by-name/li/libtcod/package.nix
diff --git a/pkgs/development/libraries/libverto/default.nix b/pkgs/by-name/li/libverto/package.nix
similarity index 100%
rename from pkgs/development/libraries/libverto/default.nix
rename to pkgs/by-name/li/libverto/package.nix
diff --git a/pkgs/development/libraries/libz/default.nix b/pkgs/by-name/li/libz/package.nix
similarity index 100%
rename from pkgs/development/libraries/libz/default.nix
rename to pkgs/by-name/li/libz/package.nix
diff --git a/pkgs/development/interpreters/lolcode/default.nix b/pkgs/by-name/lo/lolcode/package.nix
similarity index 100%
rename from pkgs/development/interpreters/lolcode/default.nix
rename to pkgs/by-name/lo/lolcode/package.nix
diff --git a/pkgs/applications/window-managers/lwm/default.nix b/pkgs/by-name/lw/lwm/package.nix
similarity index 100%
rename from pkgs/applications/window-managers/lwm/default.nix
rename to pkgs/by-name/lw/lwm/package.nix
diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/by-name/ma/magic-vlsi/package.nix
similarity index 100%
rename from pkgs/applications/science/electronics/magic-vlsi/default.nix
rename to pkgs/by-name/ma/magic-vlsi/package.nix
diff --git a/pkgs/development/compilers/marst/default.nix b/pkgs/by-name/ma/marst/package.nix
similarity index 100%
rename from pkgs/development/compilers/marst/default.nix
rename to pkgs/by-name/ma/marst/package.nix
diff --git a/pkgs/development/compilers/mcpp/default.nix b/pkgs/by-name/mc/mcpp/package.nix
similarity index 100%
rename from pkgs/development/compilers/mcpp/default.nix
rename to pkgs/by-name/mc/mcpp/package.nix
diff --git a/pkgs/development/compilers/mcpp/readlink.patch b/pkgs/by-name/mc/mcpp/readlink.patch
similarity index 100%
rename from pkgs/development/compilers/mcpp/readlink.patch
rename to pkgs/by-name/mc/mcpp/readlink.patch
diff --git a/pkgs/development/tools/literate-programming/md-tangle/default.nix b/pkgs/by-name/md/md-tangle/package.nix
similarity index 100%
rename from pkgs/development/tools/literate-programming/md-tangle/default.nix
rename to pkgs/by-name/md/md-tangle/package.nix
diff --git a/pkgs/development/libraries/mdds/default.nix b/pkgs/by-name/md/mdds/package.nix
similarity index 100%
rename from pkgs/development/libraries/mdds/default.nix
rename to pkgs/by-name/md/mdds/package.nix
diff --git a/pkgs/tools/networking/megatools/default.nix b/pkgs/by-name/me/megatools/package.nix
similarity index 100%
rename from pkgs/tools/networking/megatools/default.nix
rename to pkgs/by-name/me/megatools/package.nix
diff --git a/pkgs/by-name/mi/minijinja/package.nix b/pkgs/by-name/mi/minijinja/package.nix
index 84aa6de0ba0d..9f4eabc4886e 100644
--- a/pkgs/by-name/mi/minijinja/package.nix
+++ b/pkgs/by-name/mi/minijinja/package.nix
@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "minijinja";
-  version = "2.2.0";
+  version = "2.3.0";
 
   src = fetchFromGitHub {
     owner = "mitsuhiko";
     repo = "minijinja";
     rev = version;
-    hash = "sha256-ctFer7KPvES/tSV2e3G3rRIe7z2U4wgViB2qxBZuTUM=";
+    hash = "sha256-SZWVvj/tGpoC740An/sgdPVg+uV39QBj7qbjK0lSYdo=";
   };
 
-  cargoHash = "sha256-kDWmUg86aZP99ebkv/1aKT2YJv7DdTT5oxnegxpD9gQ=";
+  cargoHash = "sha256-OVpqfwu5x/XfqgB8xJY+qZYQUgsa2QO9FZ+/KVYZxgE=";
 
   # The tests relies on the presence of network connection
   doCheck = false;
diff --git a/pkgs/os-specific/linux/msr/000-include-sysmacros.patch b/pkgs/by-name/ms/msr/000-include-sysmacros.patch
similarity index 100%
rename from pkgs/os-specific/linux/msr/000-include-sysmacros.patch
rename to pkgs/by-name/ms/msr/000-include-sysmacros.patch
diff --git a/pkgs/os-specific/linux/msr/default.nix b/pkgs/by-name/ms/msr/package.nix
similarity index 100%
rename from pkgs/os-specific/linux/msr/default.nix
rename to pkgs/by-name/ms/msr/package.nix
diff --git a/pkgs/tools/typesetting/multimarkdown/default.nix b/pkgs/by-name/mu/multimarkdown/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/multimarkdown/default.nix
rename to pkgs/by-name/mu/multimarkdown/package.nix
diff --git a/pkgs/development/tools/build-managers/muon/default.nix b/pkgs/by-name/mu/muon/package.nix
similarity index 100%
rename from pkgs/development/tools/build-managers/muon/default.nix
rename to pkgs/by-name/mu/muon/package.nix
diff --git a/pkgs/development/libraries/nanoflann/default.nix b/pkgs/by-name/na/nanoflann/package.nix
similarity index 100%
rename from pkgs/development/libraries/nanoflann/default.nix
rename to pkgs/by-name/na/nanoflann/package.nix
diff --git a/pkgs/development/libraries/notcurses/default.nix b/pkgs/by-name/no/notcurses/package.nix
similarity index 100%
rename from pkgs/development/libraries/notcurses/default.nix
rename to pkgs/by-name/no/notcurses/package.nix
diff --git a/pkgs/applications/misc/notejot/default.nix b/pkgs/by-name/no/notejot/package.nix
similarity index 100%
rename from pkgs/applications/misc/notejot/default.nix
rename to pkgs/by-name/no/notejot/package.nix
diff --git a/pkgs/development/tools/literate-programming/nuweb/default.nix b/pkgs/by-name/nu/nuweb/package.nix
similarity index 100%
rename from pkgs/development/tools/literate-programming/nuweb/default.nix
rename to pkgs/by-name/nu/nuweb/package.nix
diff --git a/pkgs/data/fonts/office-code-pro/default.nix b/pkgs/by-name/of/office-code-pro/package.nix
similarity index 100%
rename from pkgs/data/fonts/office-code-pro/default.nix
rename to pkgs/by-name/of/office-code-pro/package.nix
diff --git a/pkgs/tools/wayland/oguri/default.nix b/pkgs/by-name/og/oguri/package.nix
similarity index 100%
rename from pkgs/tools/wayland/oguri/default.nix
rename to pkgs/by-name/og/oguri/package.nix
diff --git a/pkgs/applications/emulators/openmsx/custom-nix.mk b/pkgs/by-name/op/openmsx/custom-nix.mk
similarity index 100%
rename from pkgs/applications/emulators/openmsx/custom-nix.mk
rename to pkgs/by-name/op/openmsx/custom-nix.mk
diff --git a/pkgs/applications/emulators/openmsx/default.nix b/pkgs/by-name/op/openmsx/package.nix
similarity index 100%
rename from pkgs/applications/emulators/openmsx/default.nix
rename to pkgs/by-name/op/openmsx/package.nix
diff --git a/pkgs/tools/security/paperkey/default.nix b/pkgs/by-name/pa/paperkey/package.nix
similarity index 100%
rename from pkgs/tools/security/paperkey/default.nix
rename to pkgs/by-name/pa/paperkey/package.nix
diff --git a/pkgs/development/compilers/pforth/default.nix b/pkgs/by-name/pf/pforth/package.nix
similarity index 100%
rename from pkgs/development/compilers/pforth/default.nix
rename to pkgs/by-name/pf/pforth/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-pie.nix b/pkgs/by-name/pg/pgf-pie/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-pie.nix
rename to pkgs/by-name/pg/pgf-pie/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-umlcd.nix b/pkgs/by-name/pg/pgf-umlcd/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-umlcd.nix
rename to pkgs/by-name/pg/pgf-umlcd/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-umlsd.nix b/pkgs/by-name/pg/pgf-umlsd/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-umlsd.nix
rename to pkgs/by-name/pg/pgf-umlsd/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-1.x.nix b/pkgs/by-name/pg/pgf1/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-1.x.nix
rename to pkgs/by-name/pg/pgf1/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-2.x.nix b/pkgs/by-name/pg/pgf2/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-2.x.nix
rename to pkgs/by-name/pg/pgf2/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgf-3.x.nix b/pkgs/by-name/pg/pgf3/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgf-3.x.nix
rename to pkgs/by-name/pg/pgf3/package.nix
diff --git a/pkgs/tools/typesetting/tex/pgf-tikz/pgfplots.nix b/pkgs/by-name/pg/pgfplots/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/tex/pgf-tikz/pgfplots.nix
rename to pkgs/by-name/pg/pgfplots/package.nix
diff --git a/pkgs/applications/editors/poke/default.nix b/pkgs/by-name/po/poke/package.nix
similarity index 100%
rename from pkgs/applications/editors/poke/default.nix
rename to pkgs/by-name/po/poke/package.nix
diff --git a/pkgs/development/libraries/qrcodegen/default.nix b/pkgs/by-name/qr/qrcodegen/package.nix
similarity index 100%
rename from pkgs/development/libraries/qrcodegen/default.nix
rename to pkgs/by-name/qr/qrcodegen/package.nix
diff --git a/pkgs/by-name/qu/quick-lookup/package.nix b/pkgs/by-name/qu/quick-lookup/package.nix
new file mode 100644
index 000000000000..ffd8d48a2c51
--- /dev/null
+++ b/pkgs/by-name/qu/quick-lookup/package.nix
@@ -0,0 +1,57 @@
+{
+  lib,
+  stdenv,
+  fetchFromGitHub,
+  meson,
+  ninja,
+  pkg-config,
+  gobject-introspection,
+  wrapGAppsHook4,
+  desktop-file-utils,
+  libadwaita,
+  gjs,
+  webkitgtk_6_0,
+  glib-networking,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "quick-lookup";
+  version = "2.1.1";
+
+  src = fetchFromGitHub {
+    owner = "johnfactotum";
+    repo = "quick-lookup";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-I6a8J/Z1yJhdqWES+1mIlvJq6FBOX0GiW0muNP/iSjE=";
+  };
+
+  postPatch = ''
+    substituteInPlace post_install.py \
+      --replace-fail 'gtk-update-icon-cache' 'gtk4-update-icon-cache'
+  '';
+
+  nativeBuildInputs = [
+    meson
+    ninja
+    pkg-config
+    gobject-introspection
+    wrapGAppsHook4
+    desktop-file-utils
+  ];
+
+  buildInputs = [
+    libadwaita
+    gjs
+    webkitgtk_6_0
+    glib-networking
+  ];
+
+  meta = {
+    description = "Simple GTK dictionary application powered by Wiktionary";
+    homepage = "https://github.com/johnfactotum/quick-lookup";
+    license = lib.licenses.gpl3Plus;
+    mainProgram = "quick-lookup";
+    maintainers = with lib.maintainers; [ aleksana ];
+    platforms = lib.platforms.linux;
+  };
+})
diff --git a/pkgs/development/interpreters/quickjs/default.nix b/pkgs/by-name/qu/quickjs/package.nix
similarity index 100%
rename from pkgs/development/interpreters/quickjs/default.nix
rename to pkgs/by-name/qu/quickjs/package.nix
diff --git a/pkgs/tools/misc/rcm/fix-rcmlib-path.patch b/pkgs/by-name/rc/rcm/fix-rcmlib-path.patch
similarity index 100%
rename from pkgs/tools/misc/rcm/fix-rcmlib-path.patch
rename to pkgs/by-name/rc/rcm/fix-rcmlib-path.patch
diff --git a/pkgs/tools/misc/rcm/default.nix b/pkgs/by-name/rc/rcm/package.nix
similarity index 100%
rename from pkgs/tools/misc/rcm/default.nix
rename to pkgs/by-name/rc/rcm/package.nix
diff --git a/pkgs/tools/misc/recutils/default.nix b/pkgs/by-name/re/recutils/package.nix
similarity index 100%
rename from pkgs/tools/misc/recutils/default.nix
rename to pkgs/by-name/re/recutils/package.nix
diff --git a/pkgs/tools/bootloaders/refind/0001-toolchain.patch b/pkgs/by-name/re/refind/0001-toolchain.patch
similarity index 100%
rename from pkgs/tools/bootloaders/refind/0001-toolchain.patch
rename to pkgs/by-name/re/refind/0001-toolchain.patch
diff --git a/pkgs/tools/bootloaders/refind/0002-preserve-dates.patch b/pkgs/by-name/re/refind/0002-preserve-dates.patch
similarity index 100%
rename from pkgs/tools/bootloaders/refind/0002-preserve-dates.patch
rename to pkgs/by-name/re/refind/0002-preserve-dates.patch
diff --git a/pkgs/tools/bootloaders/refind/default.nix b/pkgs/by-name/re/refind/package.nix
similarity index 100%
rename from pkgs/tools/bootloaders/refind/default.nix
rename to pkgs/by-name/re/refind/package.nix
diff --git a/pkgs/development/libraries/rep-gtk/default.nix b/pkgs/by-name/re/rep-gtk/package.nix
similarity index 100%
rename from pkgs/development/libraries/rep-gtk/default.nix
rename to pkgs/by-name/re/rep-gtk/package.nix
diff --git a/pkgs/development/libraries/rep-gtk/setup-hook.sh b/pkgs/by-name/re/rep-gtk/setup-hook.sh
similarity index 100%
rename from pkgs/development/libraries/rep-gtk/setup-hook.sh
rename to pkgs/by-name/re/rep-gtk/setup-hook.sh
diff --git a/pkgs/tools/misc/rockbox-utility/default.nix b/pkgs/by-name/ro/rockbox-utility/package.nix
similarity index 100%
rename from pkgs/tools/misc/rockbox-utility/default.nix
rename to pkgs/by-name/ro/rockbox-utility/package.nix
diff --git a/pkgs/applications/misc/rootbar/default.nix b/pkgs/by-name/ro/rootbar/package.nix
similarity index 100%
rename from pkgs/applications/misc/rootbar/default.nix
rename to pkgs/by-name/ro/rootbar/package.nix
diff --git a/pkgs/applications/emulators/rpcemu/default.nix b/pkgs/by-name/rp/rpcemu/package.nix
similarity index 100%
rename from pkgs/applications/emulators/rpcemu/default.nix
rename to pkgs/by-name/rp/rpcemu/package.nix
diff --git a/pkgs/applications/terminal-emulators/rxvt/default.nix b/pkgs/by-name/rx/rxvt/package.nix
similarity index 100%
rename from pkgs/applications/terminal-emulators/rxvt/default.nix
rename to pkgs/by-name/rx/rxvt/package.nix
diff --git a/pkgs/applications/terminal-emulators/sakura/default.nix b/pkgs/by-name/sa/sakura/package.nix
similarity index 100%
rename from pkgs/applications/terminal-emulators/sakura/default.nix
rename to pkgs/by-name/sa/sakura/package.nix
diff --git a/pkgs/development/tools/build-managers/samurai/default.nix b/pkgs/by-name/sa/samurai/package.nix
similarity index 100%
rename from pkgs/development/tools/build-managers/samurai/default.nix
rename to pkgs/by-name/sa/samurai/package.nix
diff --git a/pkgs/applications/window-managers/sawfish/default.nix b/pkgs/by-name/sa/sawfish/package.nix
similarity index 100%
rename from pkgs/applications/window-managers/sawfish/default.nix
rename to pkgs/by-name/sa/sawfish/package.nix
diff --git a/pkgs/applications/file-managers/shfm/default.nix b/pkgs/by-name/sh/shfm/package.nix
similarity index 100%
rename from pkgs/applications/file-managers/shfm/default.nix
rename to pkgs/by-name/sh/shfm/package.nix
diff --git a/pkgs/applications/emulators/simh/default.nix b/pkgs/by-name/si/simh/package.nix
similarity index 100%
rename from pkgs/applications/emulators/simh/default.nix
rename to pkgs/by-name/si/simh/package.nix
diff --git a/pkgs/tools/typesetting/skribilo/default.nix b/pkgs/by-name/sk/skribilo/package.nix
similarity index 100%
rename from pkgs/tools/typesetting/skribilo/default.nix
rename to pkgs/by-name/sk/skribilo/package.nix
diff --git a/pkgs/development/libraries/slang/default.nix b/pkgs/by-name/sl/slang/package.nix
similarity index 100%
rename from pkgs/development/libraries/slang/default.nix
rename to pkgs/by-name/sl/slang/package.nix
diff --git a/pkgs/tools/wayland/stacktile/default.nix b/pkgs/by-name/st/stacktile/package.nix
similarity index 100%
rename from pkgs/tools/wayland/stacktile/default.nix
rename to pkgs/by-name/st/stacktile/package.nix
diff --git a/pkgs/tools/graphics/steghide/default.nix b/pkgs/by-name/st/steghide/package.nix
similarity index 100%
rename from pkgs/tools/graphics/steghide/default.nix
rename to pkgs/by-name/st/steghide/package.nix
diff --git a/pkgs/applications/audio/tap-plugins/default.nix b/pkgs/by-name/ta/tap-plugins/package.nix
similarity index 100%
rename from pkgs/applications/audio/tap-plugins/default.nix
rename to pkgs/by-name/ta/tap-plugins/package.nix
diff --git a/pkgs/applications/networking/ftp/taxi/default.nix b/pkgs/by-name/ta/taxi/package.nix
similarity index 100%
rename from pkgs/applications/networking/ftp/taxi/default.nix
rename to pkgs/by-name/ta/taxi/package.nix
diff --git a/pkgs/applications/office/teapot/001-fix-warning.patch b/pkgs/by-name/te/teapot/001-fix-warning.patch
similarity index 100%
rename from pkgs/applications/office/teapot/001-fix-warning.patch
rename to pkgs/by-name/te/teapot/001-fix-warning.patch
diff --git a/pkgs/applications/office/teapot/002-remove-help.patch b/pkgs/by-name/te/teapot/002-remove-help.patch
similarity index 100%
rename from pkgs/applications/office/teapot/002-remove-help.patch
rename to pkgs/by-name/te/teapot/002-remove-help.patch
diff --git a/pkgs/applications/office/teapot/default.nix b/pkgs/by-name/te/teapot/package.nix
similarity index 100%
rename from pkgs/applications/office/teapot/default.nix
rename to pkgs/by-name/te/teapot/package.nix
diff --git a/pkgs/applications/emulators/tiny8086/default.nix b/pkgs/by-name/ti/tiny8086/package.nix
similarity index 100%
rename from pkgs/applications/emulators/tiny8086/default.nix
rename to pkgs/by-name/ti/tiny8086/package.nix
diff --git a/pkgs/development/libraries/tllist/default.nix b/pkgs/by-name/tl/tllist/package.nix
similarity index 100%
rename from pkgs/development/libraries/tllist/default.nix
rename to pkgs/by-name/tl/tllist/package.nix
diff --git a/pkgs/applications/misc/tomato-c/default.nix b/pkgs/by-name/to/tomato-c/package.nix
similarity index 100%
rename from pkgs/applications/misc/tomato-c/default.nix
rename to pkgs/by-name/to/tomato-c/package.nix
diff --git a/pkgs/development/libraries/toml11/default.nix b/pkgs/by-name/to/toml11/package.nix
similarity index 100%
rename from pkgs/development/libraries/toml11/default.nix
rename to pkgs/by-name/to/toml11/package.nix
diff --git a/pkgs/development/libraries/tomlc99/default.nix b/pkgs/by-name/to/tomlc99/package.nix
similarity index 100%
rename from pkgs/development/libraries/tomlc99/default.nix
rename to pkgs/by-name/to/tomlc99/package.nix
diff --git a/pkgs/development/libraries/tomlcpp/default.nix b/pkgs/by-name/to/tomlcpp/package.nix
similarity index 100%
rename from pkgs/development/libraries/tomlcpp/default.nix
rename to pkgs/by-name/to/tomlcpp/package.nix
diff --git a/pkgs/tools/misc/triehash/default.nix b/pkgs/by-name/tr/triehash/package.nix
similarity index 100%
rename from pkgs/tools/misc/triehash/default.nix
rename to pkgs/by-name/tr/triehash/package.nix
diff --git a/pkgs/applications/misc/tty-solitaire/default.nix b/pkgs/by-name/tt/tty-solitaire/package.nix
similarity index 100%
rename from pkgs/applications/misc/tty-solitaire/default.nix
rename to pkgs/by-name/tt/tty-solitaire/package.nix
diff --git a/pkgs/development/libraries/twolame/default.nix b/pkgs/by-name/tw/twolame/package.nix
similarity index 100%
rename from pkgs/development/libraries/twolame/default.nix
rename to pkgs/by-name/tw/twolame/package.nix
diff --git a/pkgs/applications/misc/udevil/device-info-sys-stat.patch b/pkgs/by-name/ud/udevil/device-info-sys-stat.patch
similarity index 100%
rename from pkgs/applications/misc/udevil/device-info-sys-stat.patch
rename to pkgs/by-name/ud/udevil/device-info-sys-stat.patch
diff --git a/pkgs/applications/misc/udevil/default.nix b/pkgs/by-name/ud/udevil/package.nix
similarity index 100%
rename from pkgs/applications/misc/udevil/default.nix
rename to pkgs/by-name/ud/udevil/package.nix
diff --git a/pkgs/applications/misc/udiskie/locale-path.patch b/pkgs/by-name/ud/udiskie/locale-path.patch
similarity index 100%
rename from pkgs/applications/misc/udiskie/locale-path.patch
rename to pkgs/by-name/ud/udiskie/locale-path.patch
diff --git a/pkgs/applications/misc/udiskie/default.nix b/pkgs/by-name/ud/udiskie/package.nix
similarity index 100%
rename from pkgs/applications/misc/udiskie/default.nix
rename to pkgs/by-name/ud/udiskie/package.nix
diff --git a/pkgs/development/libraries/udunits/default.nix b/pkgs/by-name/ud/udunits/package.nix
similarity index 100%
rename from pkgs/development/libraries/udunits/default.nix
rename to pkgs/by-name/ud/udunits/package.nix
diff --git a/pkgs/development/tools/misc/universal-ctags/000-nixos-specific.patch b/pkgs/by-name/un/universal-ctags/000-nixos-specific.patch
similarity index 100%
rename from pkgs/development/tools/misc/universal-ctags/000-nixos-specific.patch
rename to pkgs/by-name/un/universal-ctags/000-nixos-specific.patch
diff --git a/pkgs/development/tools/misc/universal-ctags/default.nix b/pkgs/by-name/un/universal-ctags/package.nix
similarity index 100%
rename from pkgs/development/tools/misc/universal-ctags/default.nix
rename to pkgs/by-name/un/universal-ctags/package.nix
diff --git a/pkgs/tools/archivers/unzoo/default.nix b/pkgs/by-name/un/unzoo/package.nix
similarity index 100%
rename from pkgs/tools/archivers/unzoo/default.nix
rename to pkgs/by-name/un/unzoo/package.nix
diff --git a/pkgs/tools/misc/urjtag/default.nix b/pkgs/by-name/ur/urjtag/package.nix
similarity index 100%
rename from pkgs/tools/misc/urjtag/default.nix
rename to pkgs/by-name/ur/urjtag/package.nix
diff --git a/pkgs/applications/misc/variety/default.nix b/pkgs/by-name/va/variety/package.nix
similarity index 100%
rename from pkgs/applications/misc/variety/default.nix
rename to pkgs/by-name/va/variety/package.nix
diff --git a/pkgs/by-name/vi/villain/package.nix b/pkgs/by-name/vi/villain/package.nix
index 35db4e3d3b7f..ab40f15b50ae 100644
--- a/pkgs/by-name/vi/villain/package.nix
+++ b/pkgs/by-name/vi/villain/package.nix
@@ -8,14 +8,14 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "villain";
-  version = "2.1.0";
+  version = "2.2.0";
   pyproject = false;
 
   src = fetchFromGitHub {
     owner = "t3l3machus";
     repo = "Villain";
     rev = "v${version}";
-    hash = "sha256-8MOpbyw4HEJMcv84bNkNLBSZfEmIm3RDSUi0s62t9ko=";
+    hash = "sha256-7qZ91WEzQg9k9V/FlREW4YLlEnloeVkisDO8q/+bheo=";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/editors/viw/default.nix b/pkgs/by-name/vi/viw/package.nix
similarity index 100%
rename from pkgs/applications/editors/viw/default.nix
rename to pkgs/by-name/vi/viw/package.nix
diff --git a/pkgs/tools/graphics/wallutils/000-add-nixos-dirs-to-default-wallpapers.patch b/pkgs/by-name/wa/wallutils/000-add-nixos-dirs-to-default-wallpapers.patch
similarity index 100%
rename from pkgs/tools/graphics/wallutils/000-add-nixos-dirs-to-default-wallpapers.patch
rename to pkgs/by-name/wa/wallutils/000-add-nixos-dirs-to-default-wallpapers.patch
diff --git a/pkgs/tools/graphics/wallutils/default.nix b/pkgs/by-name/wa/wallutils/package.nix
similarity index 100%
rename from pkgs/tools/graphics/wallutils/default.nix
rename to pkgs/by-name/wa/wallutils/package.nix
diff --git a/pkgs/by-name/wa/warp-terminal/versions.json b/pkgs/by-name/wa/warp-terminal/versions.json
index 721759572aea..5faab954c316 100644
--- a/pkgs/by-name/wa/warp-terminal/versions.json
+++ b/pkgs/by-name/wa/warp-terminal/versions.json
@@ -1,14 +1,14 @@
 {
   "darwin": {
-    "hash": "sha256-EDu3BwNvCsy11pycqwDasSdV1g50fFQCa2eaax3mGTg=",
-    "version": "0.2024.09.03.08.02.stable_03"
+    "hash": "sha256-nED8SIfrxlKKT4J88L1Vnpq4Iq6TA4QMFK9TQfX4uRk=",
+    "version": "0.2024.09.10.08.02.stable_01"
   },
   "linux_x86_64": {
-    "hash": "sha256-yG7Gr2B5VqDuZfB4RJZYZNt7SNOJ2HSwSCM+1iKhshc=",
-    "version": "0.2024.09.03.08.02.stable_03"
+    "hash": "sha256-fNy0cNNgpq3JoeZhN20/7pRwCf53DwGkHl92/974FLQ=",
+    "version": "0.2024.09.10.08.02.stable_01"
   },
   "linux_aarch64": {
-    "hash": "sha256-gg5ACoABFesDUhdVBOlv+bQtliQ3N/RZlmzDMuONef8=",
-    "version": "0.2024.09.03.08.02.stable_03"
+    "hash": "sha256-HlPR3Q94KEdVlBsy2L+GQcyQ1qxw+As6qhWF5N3n3i4=",
+    "version": "0.2024.09.10.08.02.stable_01"
   }
 }
diff --git a/pkgs/tools/networking/wifish/default.nix b/pkgs/by-name/wi/wifish/package.nix
similarity index 100%
rename from pkgs/tools/networking/wifish/default.nix
rename to pkgs/by-name/wi/wifish/package.nix
diff --git a/pkgs/applications/misc/with-shell/default.nix b/pkgs/by-name/wi/with-shell/package.nix
similarity index 100%
rename from pkgs/applications/misc/with-shell/default.nix
rename to pkgs/by-name/wi/with-shell/package.nix
diff --git a/pkgs/tools/wayland/wlay/default.nix b/pkgs/by-name/wl/wlay/package.nix
similarity index 100%
rename from pkgs/tools/wayland/wlay/default.nix
rename to pkgs/by-name/wl/wlay/package.nix
diff --git a/pkgs/development/compilers/xa/xa.nix b/pkgs/by-name/xa/xa/package.nix
similarity index 100%
rename from pkgs/development/compilers/xa/xa.nix
rename to pkgs/by-name/xa/xa/package.nix
diff --git a/pkgs/applications/misc/xiphos/0001-Add-dbus-glib-dependency-to-main.patch b/pkgs/by-name/xi/xiphos/0001-Add-dbus-glib-dependency-to-main.patch
similarity index 100%
rename from pkgs/applications/misc/xiphos/0001-Add-dbus-glib-dependency-to-main.patch
rename to pkgs/by-name/xi/xiphos/0001-Add-dbus-glib-dependency-to-main.patch
diff --git a/pkgs/applications/misc/xiphos/default.nix b/pkgs/by-name/xi/xiphos/package.nix
similarity index 100%
rename from pkgs/applications/misc/xiphos/default.nix
rename to pkgs/by-name/xi/xiphos/package.nix
diff --git a/pkgs/development/interpreters/yabasic/default.nix b/pkgs/by-name/ya/yabasic/package.nix
similarity index 100%
rename from pkgs/development/interpreters/yabasic/default.nix
rename to pkgs/by-name/ya/yabasic/package.nix
diff --git a/pkgs/applications/misc/yambar/default.nix b/pkgs/by-name/ya/yambar/package.nix
similarity index 100%
rename from pkgs/applications/misc/yambar/default.nix
rename to pkgs/by-name/ya/yambar/package.nix
diff --git a/pkgs/development/interpreters/yex-lang/default.nix b/pkgs/by-name/ye/yex-lang/package.nix
similarity index 100%
rename from pkgs/development/interpreters/yex-lang/default.nix
rename to pkgs/by-name/ye/yex-lang/package.nix
diff --git a/pkgs/by-name/ze/zed-editor/Cargo.lock b/pkgs/by-name/ze/zed-editor/Cargo.lock
index 7b37eb85391b..4a6bdbddb433 100644
--- a/pkgs/by-name/ze/zed-editor/Cargo.lock
+++ b/pkgs/by-name/ze/zed-editor/Cargo.lock
@@ -14197,7 +14197,7 @@ dependencies = [
 
 [[package]]
 name = "zed"
-version = "0.152.3"
+version = "0.152.4"
 dependencies = [
  "activity_indicator",
  "anyhow",
diff --git a/pkgs/by-name/ze/zed-editor/package.nix b/pkgs/by-name/ze/zed-editor/package.nix
index d3e5ac0cba5d..d9e240d6c1a9 100644
--- a/pkgs/by-name/ze/zed-editor/package.nix
+++ b/pkgs/by-name/ze/zed-editor/package.nix
@@ -85,13 +85,13 @@ let
 in
 rustPlatform.buildRustPackage rec {
   pname = "zed";
-  version = "0.152.3";
+  version = "0.152.4";
 
   src = fetchFromGitHub {
     owner = "zed-industries";
     repo = "zed";
     rev = "refs/tags/v${version}";
-    hash = "sha256-0goeDz0mrZGPxsU51WGJz0mG5hdbY/75l/1Dyg2JLl4=";
+    hash = "sha256-nmnhJQ8DDKuy0DBfQCEj9FsVXre/gTkIsr5UjiiWasU=";
     fetchSubmodules = true;
   };
 
diff --git a/pkgs/applications/editors/zile/default.nix b/pkgs/by-name/zi/zile/package.nix
similarity index 100%
rename from pkgs/applications/editors/zile/default.nix
rename to pkgs/by-name/zi/zile/package.nix
diff --git a/pkgs/development/libraries/zxing-cpp/default.nix b/pkgs/by-name/zx/zxing-cpp/package.nix
similarity index 100%
rename from pkgs/development/libraries/zxing-cpp/default.nix
rename to pkgs/by-name/zx/zxing-cpp/package.nix
diff --git a/pkgs/development/libraries/zydis/default.nix b/pkgs/by-name/zy/zydis/package.nix
similarity index 100%
rename from pkgs/development/libraries/zydis/default.nix
rename to pkgs/by-name/zy/zydis/package.nix
diff --git a/pkgs/development/libraries/zydis/zycore.nix b/pkgs/by-name/zy/zydis/zycore.nix
similarity index 100%
rename from pkgs/development/libraries/zydis/zycore.nix
rename to pkgs/by-name/zy/zydis/zycore.nix
diff --git a/pkgs/development/libraries/zziplib/default.nix b/pkgs/by-name/zz/zziplib/package.nix
similarity index 100%
rename from pkgs/development/libraries/zziplib/default.nix
rename to pkgs/by-name/zz/zziplib/package.nix
diff --git a/pkgs/desktops/plasma-5/default.nix b/pkgs/desktops/plasma-5/default.nix
index b1fa8a7068a1..20c7904f9c0a 100644
--- a/pkgs/desktops/plasma-5/default.nix
+++ b/pkgs/desktops/plasma-5/default.nix
@@ -28,7 +28,6 @@
 , lib
 , config
 , fetchurl
-, gconf
 , gsettings-desktop-schemas
 }:
 
@@ -156,7 +155,7 @@ let
       plasma-mobile = callPackage ./plasma-mobile { };
       plasma-nano = callPackage ./plasma-nano { };
       plasma-nm = callPackage ./plasma-nm { };
-      plasma-pa = callPackage ./plasma-pa.nix { inherit gconf; };
+      plasma-pa = callPackage ./plasma-pa.nix { };
       plasma-remotecontrollers = callPackage ./plasma-remotecontrollers.nix { };
       plasma-sdk = callPackage ./plasma-sdk.nix { };
       plasma-systemmonitor = callPackage ./plasma-systemmonitor.nix { };
diff --git a/pkgs/desktops/plasma-5/plasma-pa.nix b/pkgs/desktops/plasma-5/plasma-pa.nix
index 0256461db94c..40a05ed6fe14 100644
--- a/pkgs/desktops/plasma-5/plasma-pa.nix
+++ b/pkgs/desktops/plasma-5/plasma-pa.nix
@@ -11,7 +11,6 @@
 , plasma-framework
 , qtbase
 , qtdeclarative
-, gconf
 , glib
 , libcanberra-gtk3
 , libpulseaudio
@@ -22,7 +21,6 @@ mkDerivation {
   pname = "plasma-pa";
   nativeBuildInputs = [ extra-cmake-modules kdoctools ];
   buildInputs = [
-    gconf
     glib
     libcanberra-gtk3
     libpulseaudio
diff --git a/pkgs/development/compilers/vyper/default.nix b/pkgs/development/compilers/vyper/default.nix
index 56899b6acba4..89973eb524ee 100644
--- a/pkgs/development/compilers/vyper/default.nix
+++ b/pkgs/development/compilers/vyper/default.nix
@@ -7,7 +7,6 @@
 , importlib-metadata
 , packaging
 , pycryptodome
-, pytest-runner
 , pythonOlder
 , recommonmark
 , setuptools-scm
@@ -41,7 +40,8 @@ buildPythonPackage rec {
   postPatch = ''
     # pythonRelaxDeps doesn't work
     substituteInPlace setup.py \
-      --replace "setuptools_scm>=7.1.0,<8.0.0" "setuptools_scm>=7.1.0"
+      --replace-fail "setuptools_scm>=7.1.0,<8.0.0" "setuptools_scm>=7.1.0" \
+      --replace-fail '"pytest-runner",' ""
   '';
 
   nativeBuildInputs = [
@@ -49,7 +49,6 @@ buildPythonPackage rec {
     # ever since https://github.com/vyperlang/vyper/pull/2816
     git
 
-    pytest-runner
     setuptools-scm
   ];
 
diff --git a/pkgs/development/libraries/psqlodbc/default.nix b/pkgs/development/libraries/psqlodbc/default.nix
index 0431bb284dab..18e6bc3b0f7d 100644
--- a/pkgs/development/libraries/psqlodbc/default.nix
+++ b/pkgs/development/libraries/psqlodbc/default.nix
@@ -10,7 +10,7 @@ stdenv.mkDerivation rec {
   version = "16.00.0000";
 
   src = fetchurl {
-    url = "https://ftp.postgresql.org/pub/odbc/versions/src/psqlodbc-${version}.tar.gz";
+    url = "https://ftp.postgresql.org/pub/odbc/versions.old/src/${pname}-${version}.tar.gz";
     hash = "sha256-r9iS+J0uzujT87IxTxvVvy0CIBhyxuNDHlwxCW7KTIs=";
   };
 
diff --git a/pkgs/development/python-modules/awslambdaric/default.nix b/pkgs/development/python-modules/awslambdaric/default.nix
index a831b5300eb9..f208c5048767 100644
--- a/pkgs/development/python-modules/awslambdaric/default.nix
+++ b/pkgs/development/python-modules/awslambdaric/default.nix
@@ -3,7 +3,6 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  fetchpatch,
   isPy27,
   pytestCheckHook,
   autoconf271,
@@ -11,14 +10,14 @@
   cmake,
   gcc,
   libtool,
+  parameterized,
   perl,
   setuptools,
   simplejson,
 }:
-
 buildPythonPackage rec {
   pname = "awslambdaric";
-  version = "2.0.11";
+  version = "2.1.0";
   pyproject = true;
 
   disabled = isPy27;
@@ -27,22 +26,9 @@ buildPythonPackage rec {
     owner = "aws";
     repo = "aws-lambda-python-runtime-interface-client";
     rev = "refs/tags/${version}";
-    sha256 = "sha256-9DiUpgeL4bY7G3b5R06FjpN0st03F84fj0bhp70moKo=";
+    sha256 = "sha256-FHZ7ZTCOzElW/DM07TScp6bfOOFe4b307q/ALVX1fWQ=";
   };
 
-  patches = [
-    (fetchpatch {
-      # https://github.com/aws/aws-lambda-python-runtime-interface-client/pull/58
-      url = "https://github.com/aws/aws-lambda-python-runtime-interface-client/commit/162c3c0051bb9daa92e4a2a4af7e90aea60ee405.patch";
-      sha256 = "09qqq5x6npc9jw2qbhzifqn5sqiby4smiin1aw30psmlp21fv7j8";
-    })
-  ];
-
-  postPatch = ''
-    substituteInPlace requirements/base.txt \
-      --replace 'simplejson==3' 'simplejson~=3'
-  '';
-
   propagatedBuildInputs = [ simplejson ];
 
   nativeBuildInputs = [
@@ -58,11 +44,9 @@ buildPythonPackage rec {
 
   dontUseCmakeConfigure = true;
 
-  nativeCheckInputs = [ pytestCheckHook ];
-
-  disabledTests = [
-    # Test fails with: Assertion error
-    "test_handle_event_request_fault_exception_logging_syntax_error"
+  nativeCheckInputs = [
+    parameterized
+    pytestCheckHook
   ];
 
   pythonImportsCheck = [
@@ -71,7 +55,7 @@ buildPythonPackage rec {
   ];
 
   meta = with lib; {
-    broken = (stdenv.isLinux && stdenv.isAarch64);
+    broken = stdenv.isLinux && stdenv.isAarch64;
     description = "AWS Lambda Runtime Interface Client for Python";
     homepage = "https://github.com/aws/aws-lambda-python-runtime-interface-client";
     license = licenses.asl20;
diff --git a/pkgs/development/python-modules/graphrag/default.nix b/pkgs/development/python-modules/graphrag/default.nix
index efd595a42efd..a5c1589a0348 100644
--- a/pkgs/development/python-modules/graphrag/default.nix
+++ b/pkgs/development/python-modules/graphrag/default.nix
@@ -40,14 +40,14 @@
 
 buildPythonPackage rec {
   pname = "graphrag";
-  version = "0.3.2";
+  version = "0.3.3";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "microsoft";
     repo = "graphrag";
     rev = "refs/tags/v${version}";
-    hash = "sha256-tfncCFQTeGpTBns+Gt/O7JnFVF5OcpWOwplD0hLWVvc=";
+    hash = "sha256-x1boxBF3fO+IqHnJx85mjYQHhEG8h03H90T0dtc3CNQ=";
   };
 
   build-system = [
diff --git a/pkgs/development/python-modules/hikari/default.nix b/pkgs/development/python-modules/hikari/default.nix
index 026176e7a7b8..dbc853b926aa 100644
--- a/pkgs/development/python-modules/hikari/default.nix
+++ b/pkgs/development/python-modules/hikari/default.nix
@@ -4,13 +4,12 @@
   fetchFromGitHub,
   pytestCheckHook,
   pythonOlder,
-  pytest-runner,
   aiohttp,
   attrs,
   multidict,
   colorlog,
   pynacl,
-  pytest-cov,
+  pytest-cov-stub,
   pytest-randomly,
   pytest-asyncio,
   mock,
@@ -52,9 +51,8 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytestCheckHook
-    pytest-runner
     pytest-asyncio
-    pytest-cov
+    pytest-cov-stub
     pytest-randomly
     mock
   ];
diff --git a/pkgs/development/python-modules/openai/default.nix b/pkgs/development/python-modules/openai/default.nix
index 2f50fadc7c69..9c54fe5daf4d 100644
--- a/pkgs/development/python-modules/openai/default.nix
+++ b/pkgs/development/python-modules/openai/default.nix
@@ -35,7 +35,7 @@
 
 buildPythonPackage rec {
   pname = "openai";
-  version = "1.44.0";
+  version = "1.45.1";
   pyproject = true;
 
   disabled = pythonOlder "3.7.1";
@@ -44,7 +44,7 @@ buildPythonPackage rec {
     owner = "openai";
     repo = "openai-python";
     rev = "refs/tags/v${version}";
-    hash = "sha256-HD7gqdWREULH0GQ1xNRh/TJEOzo82ghHC9gTrx7qxxU=";
+    hash = "sha256-2oO87J/Z3VGmBHJE2vBEvEtKa1XHQ6uWZfQTxwzHpMk=";
   };
 
   build-system = [
diff --git a/pkgs/development/python-modules/pyqt3d/default.nix b/pkgs/development/python-modules/pyqt3d/default.nix
index abf60dcad115..487ab3a10985 100644
--- a/pkgs/development/python-modules/pyqt3d/default.nix
+++ b/pkgs/development/python-modules/pyqt3d/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "pyqt3d";
-  version = "5.15.6";
+  version = "5.15.7";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "PyQt3D";
     inherit version;
-    hash = "sha256-fWxtVc2PwiGzE8mVwPhymjdxFJJvA3f46QEdRevziBw=";
+    hash = "sha256-6ng+tUbH2tLV6q+C6lBQ3eRSVamELgoddYSIHp4lqVE=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/pyqtchart/default.nix b/pkgs/development/python-modules/pyqtchart/default.nix
index 1a6675b9ad80..2ee389ad2075 100644
--- a/pkgs/development/python-modules/pyqtchart/default.nix
+++ b/pkgs/development/python-modules/pyqtchart/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "pyqtchart";
-  version = "5.15.6";
+  version = "5.15.7";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "PyQtChart";
     inherit version;
-    hash = "sha256-JpF5b+kqKUphdZKlxcNeeF3JH3dZ3vnrItp532N2Izk=";
+    hash = "sha256-vJ8dJscl6CCw//jbbpBuiyhhKKFLOpjFmgzQw9mSQJU=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/pyqtdatavisualization/default.nix b/pkgs/development/python-modules/pyqtdatavisualization/default.nix
index d0c1ba5b8d05..9fce4b02bc7d 100644
--- a/pkgs/development/python-modules/pyqtdatavisualization/default.nix
+++ b/pkgs/development/python-modules/pyqtdatavisualization/default.nix
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "pyqtdatavisualization";
-  version = "5.15.5";
+  version = "5.15.6";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -21,7 +21,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "PyQtDataVisualization";
     inherit version;
-    hash = "sha256-iSf496pwhX7wDFHj379vg92fOFX0FuDVMVknYcu53H8=";
+    hash = "sha256-ntM7IOdHvGnh1hnxR7sWJcwA1u9ATb8Ha6E6n/b2Bh0=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/pytest-harvest/default.nix b/pkgs/development/python-modules/pytest-harvest/default.nix
index 65325851b770..35e5945c1a62 100644
--- a/pkgs/development/python-modules/pytest-harvest/default.nix
+++ b/pkgs/development/python-modules/pytest-harvest/default.nix
@@ -3,7 +3,6 @@
   buildPythonPackage,
   fetchFromGitHub,
   setuptools-scm,
-  pytest-runner,
   pytest,
   decopatch,
   makefun,
@@ -34,11 +33,14 @@ buildPythonPackage rec {
   # we disable this file creation as it touches internet
   postPatch = ''
     echo "version = '${version}'" > pytest_harvest/_version.py
+
+    substituteInPlace pytest_harvest/tests/test_lazy_and_harvest.py \
+      --replace-fail "from distutils.version import LooseVersion" "from packaging.version import parse" \
+      --replace-fail "LooseVersion" "parse"
   '';
 
   nativeBuildInputs = [
     setuptools-scm
-    pytest-runner
   ];
 
   buildInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/pytest-runner/default.nix b/pkgs/development/python-modules/pytest-runner/default.nix
deleted file mode 100644
index 57b970fc98df..000000000000
--- a/pkgs/development/python-modules/pytest-runner/default.nix
+++ /dev/null
@@ -1,40 +0,0 @@
-{
-  lib,
-  buildPythonPackage,
-  fetchPypi,
-  setuptools-scm,
-  pytest,
-}:
-
-buildPythonPackage rec {
-  pname = "pytest-runner";
-  version = "6.0.1";
-  format = "pyproject";
-
-  src = fetchPypi {
-    inherit pname version;
-    hash = "sha256-cNRzlYWnAI83v0kzwBP9sye4h4paafy7MxbIiILw9Js=";
-  };
-
-  postPatch = ''
-    rm pytest.ini
-  '';
-
-  nativeBuildInputs = [
-    setuptools-scm
-    pytest
-  ];
-
-  checkPhase = ''
-    py.test tests
-  '';
-
-  # Fixture not found
-  doCheck = false;
-
-  meta = with lib; {
-    description = "Invoke py.test as distutils command with dependency resolution";
-    homepage = "https://github.com/pytest-dev/pytest-runner";
-    license = licenses.mit;
-  };
-}
diff --git a/pkgs/development/python-modules/roadlib/default.nix b/pkgs/development/python-modules/roadlib/default.nix
index c2ac5e3cba69..eaaf3eff9faf 100644
--- a/pkgs/development/python-modules/roadlib/default.nix
+++ b/pkgs/development/python-modules/roadlib/default.nix
@@ -11,14 +11,14 @@
 
 buildPythonPackage rec {
   pname = "roadlib";
-  version = "0.24.1";
+  version = "0.26.0";
   pyproject = true;
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-tQbJWHXxvjGhqGBI9nn8EL7rJcVyH095FfNSsxkrImQ=";
+    hash = "sha256-qh+xVBqQ/bkXl7Xa6w+SIkQRwIUW5ut4yosGko+8xrY=";
   };
 
   build-system = [ setuptools ];
diff --git a/pkgs/development/python-modules/tf2onnx/default.nix b/pkgs/development/python-modules/tf2onnx/default.nix
index 73c19842f103..54a837089bc8 100644
--- a/pkgs/development/python-modules/tf2onnx/default.nix
+++ b/pkgs/development/python-modules/tf2onnx/default.nix
@@ -2,7 +2,6 @@
   lib,
   buildPythonPackage,
   fetchFromGitHub,
-  pytest-runner,
   # runtime dependencies
   numpy,
   onnx,
@@ -34,9 +33,10 @@ buildPythonPackage rec {
     hash = "sha256-qtRzckw/KHWm3gjFwF+cPuBhGbfktjhYIwImwHn2CFk=";
   };
 
-  nativeBuildInputs = [
-    pytest-runner
-  ];
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "'pytest-runner'" ""
+  '';
 
   pythonRelaxDeps = [ "flatbuffers" ];
 
diff --git a/pkgs/development/tools/analysis/cpplint/default.nix b/pkgs/development/tools/analysis/cpplint/default.nix
index d9603ca0548d..b32e1cf4e678 100644
--- a/pkgs/development/tools/analysis/cpplint/default.nix
+++ b/pkgs/development/tools/analysis/cpplint/default.nix
@@ -35,7 +35,6 @@ python3Packages.buildPythonApplication rec {
 
   nativeCheckInputs = with python3Packages; [
     pytest
-    pytest-runner
   ];
 
   checkPhase = ''
diff --git a/pkgs/tools/admin/tigervnc/default.nix b/pkgs/tools/admin/tigervnc/default.nix
index c19e7b3b4f3a..e1a10334f45b 100644
--- a/pkgs/tools/admin/tigervnc/default.nix
+++ b/pkgs/tools/admin/tigervnc/default.nix
@@ -23,14 +23,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.13.1";
+  version = "1.14.0";
   pname = "tigervnc";
 
   src = fetchFromGitHub {
     owner = "TigerVNC";
     repo = "tigervnc";
     rev = "v${version}";
-    sha256 = "sha256-YSkgkk87bbHg7lJGoPBs7bfjvd1hvUeOZulFHYpXvvo=";
+    sha256 = "sha256-TgVV/4MRsQHYKpDf9L5eHMLVpdwvNy1KPDIe7xMlQ9o=";
   };
 
   postPatch = lib.optionalString stdenv.isLinux ''
@@ -38,8 +38,6 @@ stdenv.mkDerivation rec {
     fontPath=
     substituteInPlace vncviewer/vncviewer.cxx \
        --replace '"/usr/bin/ssh' '"${openssh}/bin/ssh'
-
-    cp unix/xserver21.1.1.patch unix/xserver211.patch
     source_top="$(pwd)"
   '' + ''
     # On Mac, do not build a .dmg, instead copy the .app to the source dir
@@ -66,7 +64,7 @@ stdenv.mkDerivation rec {
     tar xf ${xorg.xorgserver.src}
     cp -R xorg*/* unix/xserver
     pushd unix/xserver
-    version=$(echo ${xorg.xorgserver.name} | sed 's/.*-\([0-9]\+\).\([0-9]\+\).*/\1\2/g')
+    version=$(echo ${xorg.xorgserver.name} | sed 's/.*-\([0-9]\+\).[0-9]\+.*/\1/g')
     patch -p1 < "$source_top/unix/xserver$version.patch"
     autoreconf -vfi
     ./configure $configureFlags  --disable-devel-docs --disable-docs \
@@ -131,6 +129,8 @@ stdenv.mkDerivation rec {
     libXfont2
     libpciaccess
     libGLU
+    libXrandr
+    libXdamage
   ] ++ xorg.xorgserver.buildInputs
   );
 
diff --git a/pkgs/tools/backup/duplicity/default.nix b/pkgs/tools/backup/duplicity/default.nix
index 71d63a622d4d..da32f2323343 100644
--- a/pkgs/tools/backup/duplicity/default.nix
+++ b/pkgs/tools/backup/duplicity/default.nix
@@ -99,8 +99,7 @@ let self = python3.pkgs.buildPythonApplication rec {
     lockfile
     mock
     pexpect
-    pytest
-    pytest-runner
+    pytestCheckHook
     fasteners
   ]);
 
diff --git a/pkgs/tools/virtualization/udocker/default.nix b/pkgs/tools/virtualization/udocker/default.nix
index 8f0afedfd9cb..25ae2fe9ee33 100644
--- a/pkgs/tools/virtualization/udocker/default.nix
+++ b/pkgs/tools/virtualization/udocker/default.nix
@@ -17,6 +17,11 @@ python3Packages.buildPythonApplication rec {
     hash = "sha256-P49fkLvdCm/Eco+nD3SGM04PRQatBzq9CHlayueQetk=";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace-fail "'pytest-runner'," ""
+  '';
+
   # crun patchelf proot runc fakechroot
   # are download statistically linked during runtime
   buildInputs = [
@@ -28,7 +33,6 @@ python3Packages.buildPythonApplication rec {
   ];
 
   nativeCheckInputs = with python3Packages; [
-    pytest-runner
     pytestCheckHook
   ];
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 473a9177d76f..56322d14fa65 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -192,8 +192,6 @@ with pkgs;
     };
   } ../build-support/setup-hooks/auto-patchelf.sh;
 
-  tomato-c = callPackage ../applications/misc/tomato-c { };
-
   appflowy = callPackage ../applications/office/appflowy { };
 
   appimageTools = callPackage ../build-support/appimage { };
@@ -275,8 +273,6 @@ with pkgs;
 
   atkinson-hyperlegible = callPackage ../data/fonts/atkinson-hyperlegible { };
 
-  _0x =  callPackage ../tools/misc/0x { };
-
   automatic-timezoned = callPackage ../tools/system/automatic-timezoned { };
 
   cve = with python3Packages; toPythonApplication cvelib;
@@ -429,8 +425,6 @@ with pkgs;
   };
 
   cereal = cereal_1_3_0;
-  cereal_1_3_0 = callPackage ../development/libraries/cereal/1.3.0.nix { };
-  cereal_1_3_2 = callPackage ../development/libraries/cereal/1.3.2.nix { };
 
   cdecrypt = callPackage ../development/tools/cdecrypt { };
 
@@ -1299,7 +1293,6 @@ with pkgs;
 
   singularity-tools = callPackage ../build-support/singularity-tools { };
 
-  stacktile = callPackage ../tools/wayland/stacktile { };
 
   sirula = callPackage ../tools/wayland/sirula { };
 
@@ -1723,8 +1716,6 @@ with pkgs;
     wlroots = wlroots_0_17;
   };
 
-  gay = callPackage ../tools/misc/gay {  };
-
   elkhound = callPackage ../development/tools/elkhound { };
 
   ethq = callPackage ../os-specific/linux/ethq { };
@@ -1936,8 +1927,6 @@ with pkgs;
 
   sdbus-cpp = callPackage ../development/libraries/sdbus-cpp { };
 
-  basu = callPackage ../development/libraries/basu { };
-
   sdlookup = callPackage ../tools/security/sdlookup { };
 
   sdkmanager = with python3Packages; toPythonApplication sdkmanager;
@@ -2551,10 +2540,6 @@ with pkgs;
 
   darcnes = callPackage ../applications/emulators/darcnes { };
 
-  desmume = callPackage ../applications/emulators/desmume { };
-
-  dgen-sdl = callPackage ../applications/emulators/dgen-sdl { };
-
   dlx = callPackage ../applications/emulators/dlx { };
 
   dosbox = callPackage ../applications/emulators/dosbox {
@@ -2568,8 +2553,6 @@ with pkgs;
 
   dynamips = callPackage ../applications/emulators/dynamips { };
 
-  emu2 = callPackage ../applications/emulators/emu2 { };
-
   fceux = libsForQt5.callPackage ../applications/emulators/fceux { };
 
   firebird-emu = libsForQt5.callPackage ../applications/emulators/firebird-emu { };
@@ -2600,8 +2583,6 @@ with pkgs;
 
   gopsuinfo = callPackage ../tools/system/gopsuinfo { };
 
-  gxemul = callPackage ../applications/emulators/gxemul { };
-
   hatari = callPackage ../applications/emulators/hatari { };
 
   hostapd-mana = callPackage ../tools/networking/hostapd-mana { };
@@ -2636,8 +2617,6 @@ with pkgs;
 
   oberon-risc-emu = callPackage ../applications/emulators/oberon-risc-emu { };
 
-  openmsx = callPackage ../applications/emulators/openmsx { };
-
   packwiz = callPackage ../tools/games/minecraft/packwiz { };
 
   pcem = callPackage ../applications/emulators/pcem { };
@@ -2685,14 +2664,10 @@ with pkgs;
     withWayland = true;
   };
 
-  rpcemu = callPackage ../applications/emulators/rpcemu { };
-
   ruffle = callPackage ../applications/emulators/ruffle { };
 
   sameboy = callPackage ../applications/emulators/sameboy { };
 
-  simh = callPackage ../applications/emulators/simh { };
-
   simplenes = callPackage ../applications/emulators/simplenes { };
 
   snes9x-gtk = snes9x.override {
@@ -2705,8 +2680,6 @@ with pkgs;
 
   tilem = callPackage ../applications/emulators/tilem { };
 
-  tiny8086 = callPackage ../applications/emulators/tiny8086 { };
-
   uae = callPackage ../applications/emulators/uae { };
 
   vbam = callPackage ../applications/emulators/vbam { };
@@ -2837,8 +2810,6 @@ with pkgs;
 
   sfm = callPackage ../applications/file-managers/sfm { };
 
-  shfm = callPackage ../applications/file-managers/shfm { };
-
   spaceFM = callPackage ../applications/file-managers/spacefm { };
 
   vifm = callPackage ../applications/file-managers/vifm { };
@@ -2914,8 +2885,6 @@ with pkgs;
 
   mrxvt = callPackage ../applications/terminal-emulators/mrxvt { };
 
-  rxvt = callPackage ../applications/terminal-emulators/rxvt { };
-
   rxvt-unicode = callPackage ../applications/terminal-emulators/rxvt-unicode/wrapper.nix { };
 
   rxvt-unicode-emoji = rxvt-unicode.override {
@@ -2930,8 +2899,6 @@ with pkgs;
     emojiSupport = true;
   };
 
-  sakura = callPackage ../applications/terminal-emulators/sakura { };
-
   st = callPackage ../applications/terminal-emulators/st {
     conf = config.st.conf or null;
     patches = config.st.patches or [];
@@ -3499,8 +3466,6 @@ with pkgs;
 
   cpuid = callPackage ../os-specific/linux/cpuid { };
 
-  msr = callPackage ../os-specific/linux/msr { };
-
   ctre = callPackage ../development/libraries/ctre { };
 
   ctrtool = callPackage ../tools/archivers/ctrtool { };
@@ -4091,8 +4056,6 @@ with pkgs;
 
   bc = callPackage ../tools/misc/bc { };
 
-  gavin-bc = callPackage ../tools/misc/gavin-bc { };
-
   bdf2psf = callPackage ../tools/misc/bdf2psf { };
 
   bdf2sfd = callPackage ../tools/misc/bdf2sfd { };
@@ -4300,8 +4263,6 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) Cocoa;
   };
 
-  cue2pops = callPackage ../tools/cd-dvd/cue2pops { };
-
   cabal2nix-unwrapped = haskell.lib.compose.justStaticExecutables
     (haskellPackages.generateOptparseApplicativeCompletions [ "cabal2nix" ] haskellPackages.cabal2nix);
 
@@ -4380,8 +4341,6 @@ with pkgs;
 
   croc = callPackage ../tools/networking/croc { };
 
-  cbftp = callPackage ../tools/networking/cbftp { };
-
   cedille = callPackage ../applications/science/logic/cedille
                           { inherit (haskellPackages) alex happy Agda ghcWithPackages;
                           };
@@ -4520,8 +4479,6 @@ with pkgs;
 
   kanshi = callPackage ../tools/wayland/kanshi { };
 
-  oguri = callPackage  ../tools/wayland/oguri { };
-
   shikane = callPackage ../tools/wayland/shikane { };
 
   shotman = callPackage ../tools/wayland/shotman { };
@@ -4558,8 +4515,6 @@ with pkgs;
 
   wdt = callPackage ../applications/networking/sync/wdt { };
 
-  wlay = callPackage ../tools/wayland/wlay { };
-
   wl-clipboard = callPackage ../tools/wayland/wl-clipboard { };
 
   wl-clipboard-x11 = callPackage ../tools/wayland/wl-clipboard-x11 { };
@@ -5098,24 +5053,8 @@ with pkgs;
 
   mftrace = callPackage ../tools/typesetting/tex/mftrace { };
 
-  # Keep the old PGF since some documents don't render properly with
-  # the new one.
-  pgf1 = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-1.x.nix { };
-
-  pgf2 = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-2.x.nix { };
-
-  pgf3 = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-3.x.nix { };
-
   pgf = pgf2;
 
-  pgf-pie = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-pie.nix { };
-
-  pgf-umlcd = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-umlcd.nix { };
-
-  pgf-umlsd = callPackage ../tools/typesetting/tex/pgf-tikz/pgf-umlsd.nix { };
-
-  pgfplots = callPackage ../tools/typesetting/tex/pgf-tikz/pgfplots.nix { };
-
   pplatex = callPackage ../tools/typesetting/tex/pplatex { };
 
   tetex = callPackage ../tools/typesetting/tex/tetex { libpng = libpng12; };
@@ -5141,8 +5080,6 @@ with pkgs;
 
   futhark = haskell.lib.compose.justStaticExecutables haskellPackages.futhark;
 
-  tllist = callPackage ../development/libraries/tllist { };
-
   fcft = callPackage ../development/libraries/fcft { };
 
   fuzzel = callPackage ../applications/misc/fuzzel { };
@@ -5500,8 +5437,6 @@ with pkgs;
     python = python3;
   };
 
-  libnbd = callPackage ../development/libraries/libnbd { };
-
   libndtypes = callPackage ../development/libraries/libndtypes { };
 
   libnss-mysql = callPackage ../os-specific/linux/libnss-mysql { };
@@ -5514,8 +5449,6 @@ with pkgs;
 
   libxnd = callPackage ../development/libraries/libxnd { };
 
-  libz = callPackage ../development/libraries/libz { };
-
   libzbc = callPackage ../os-specific/linux/libzbc { };
 
   libzbd = callPackage ../os-specific/linux/libzbd { };
@@ -6388,8 +6321,6 @@ with pkgs;
 
   cglm = callPackage ../development/libraries/cglm { };
 
-  cgreen = callPackage ../development/libraries/cgreen { };
-
   chain-bench = callPackage ../tools/security/chain-bench { };
 
   chainsaw = callPackage ../tools/security/chainsaw { };
@@ -7009,8 +6940,6 @@ with pkgs;
 
   dfrs  = callPackage ../tools/system/dfrs { };
 
-  dev86 = callPackage ../development/compilers/dev86 { };
-
   diskrsync = callPackage ../tools/backup/diskrsync { };
 
   djbdns = callPackage ../tools/networking/djbdns { };
@@ -7254,8 +7183,6 @@ with pkgs;
 
   editres = callPackage ../tools/graphics/editres { };
 
-  edit = callPackage ../applications/editors/edit { };
-
   edk2-uefi-shell = callPackage ../tools/misc/edk2-uefi-shell { };
 
   edl = callPackage ../development/embedded/edl { };
@@ -7292,8 +7219,6 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) Security SystemConfiguration;
   };
 
-  magic-vlsi = callPackage ../applications/science/electronics/magic-vlsi { };
-
   mcrcon = callPackage ../tools/networking/mcrcon { };
 
   mozillavpn = qt6Packages.callPackage ../tools/networking/mozillavpn { };
@@ -7383,8 +7308,6 @@ with pkgs;
 
   wakeonlan = callPackage ../tools/networking/wakeonlan { };
 
-  wallutils = callPackage ../tools/graphics/wallutils { };
-
   wayback = callPackage ../tools/misc/wayback { };
 
   worker-build = callPackage ../development/tools/worker-build {
@@ -7852,8 +7775,6 @@ with pkgs;
 
   frostwire-bin = callPackage ../applications/networking/p2p/frostwire/frostwire-bin.nix { };
 
-  ftgl = callPackage ../development/libraries/ftgl { };
-
   ftop = callPackage ../os-specific/linux/ftop { };
 
   ftxui = callPackage ../development/libraries/ftxui { };
@@ -7908,8 +7829,6 @@ with pkgs;
 
   uniscribe = callPackage ../tools/text/uniscribe { };
 
-  calcoo = callPackage ../applications/misc/calcoo { };
-
   galculator = callPackage ../applications/misc/galculator {
     gtk = gtk3;
   };
@@ -8291,8 +8210,6 @@ with pkgs;
 
   gradience = callPackage ../applications/misc/gradience { };
 
-  grafx2 = callPackage ../applications/graphics/grafx2 { };
-
   grails = callPackage ../development/web/grails { jdk = null; };
 
   graylog-5_1 = callPackage ../tools/misc/graylog/5.1.nix { };
@@ -9105,12 +9022,8 @@ with pkgs;
 
   jumpapp = callPackage ../tools/X11/jumpapp { };
 
-  jove = callPackage ../applications/editors/jove { };
-
   jugglinglab = callPackage ../tools/misc/jugglinglab { };
 
-  jupp = callPackage ../applications/editors/jupp { };
-
   jupyter = callPackage ../applications/editors/jupyter { };
 
   jupyter-all = jupyter.override {
@@ -10187,8 +10100,6 @@ with pkgs;
 
   megacli = callPackage ../tools/misc/megacli { };
 
-  megatools = callPackage ../tools/networking/megatools { };
-
   memo = callPackage ../applications/misc/memo { };
 
   mencal = callPackage ../applications/misc/mencal { } ;
@@ -11694,8 +11605,6 @@ with pkgs;
 
   pypass = with python3Packages; toPythonApplication pypass;
 
-  teapot = callPackage ../applications/office/teapot { };
-
   ticktick = callPackage ../applications/office/ticktick { };
 
   pyditz = callPackage ../applications/misc/pyditz {
@@ -11829,8 +11738,6 @@ with pkgs;
 
   quickfix = callPackage ../development/libraries/quickfix { };
 
-  quickjs = callPackage ../development/interpreters/quickjs { };
-
   quickserve = callPackage ../tools/networking/quickserve { };
 
   quictls = callPackage ../development/libraries/quictls { };
@@ -11974,8 +11881,6 @@ with pkgs;
 
   readability-cli = callPackage ../tools/text/readability-cli { };
 
-  recutils = callPackage ../tools/misc/recutils { };
-
   recoll = libsForQt5.callPackage ../applications/search/recoll { };
 
   recoll-nox = recoll.override { withGui = false; };
@@ -12098,8 +12003,6 @@ with pkgs;
 
   roc-toolkit = callPackage ../development/libraries/audio/roc-toolkit { };
 
-  rockbox-utility = libsForQt5.callPackage ../tools/misc/rockbox-utility { };
-
   rosegarden = libsForQt5.callPackage ../applications/audio/rosegarden { };
 
   rosenpass = callPackage ../tools/networking/rosenpass  { };
@@ -12163,8 +12066,6 @@ with pkgs;
 
   runzip = callPackage ../tools/archivers/runzip { };
 
-  unzoo = callPackage ../tools/archivers/unzoo { };
-
   ruplacer = callPackage ../tools/text/ruplacer {
     inherit (darwin.apple_sdk.frameworks) Security;
   };
@@ -12506,8 +12407,6 @@ with pkgs;
 
   sipcalc = callPackage ../tools/networking/sipcalc { };
 
-  skribilo = callPackage ../tools/typesetting/skribilo { };
-
   skytemple = callPackage ../applications/misc/skytemple { };
 
   sleuthkit = callPackage ../tools/system/sleuthkit { };
@@ -13546,8 +13445,6 @@ with pkgs;
 
   vampire = callPackage ../applications/science/logic/vampire { };
 
-  variety = callPackage ../applications/misc/variety { };
-
   vdmfec = callPackage ../applications/backup/vdmfec { };
 
   vk-bootstrap = callPackage ../development/libraries/vk-bootstrap { };
@@ -13750,8 +13647,6 @@ with pkgs;
 
   whois = callPackage ../tools/networking/whois { };
 
-  wifish = callPackage ../tools/networking/wifish { };
-
   wimboot = callPackage ../tools/misc/wimboot { };
 
   wire = callPackage ../development/tools/wire { };
@@ -13828,8 +13723,6 @@ with pkgs;
 
   htmltest = callPackage ../development/tools/htmltest { };
 
-  rcm = callPackage ../tools/misc/rcm { };
-
   td = callPackage ../tools/misc/td { };
 
   tdfgo = callPackage ../tools/misc/tdfgo { };
@@ -13874,8 +13767,6 @@ with pkgs;
     libjpeg_turbo = libjpeg_turbo.override { enableJava = true; };
   };
 
-  udunits = callPackage ../development/libraries/udunits { };
-
   ufmt = with python3Packages; toPythonApplication ufmt;
 
   uftp = callPackage ../servers/uftp { };
@@ -13997,8 +13888,6 @@ with pkgs;
 
   upwork = callPackage ../applications/misc/upwork { };
 
-  urjtag = callPackage ../tools/misc/urjtag { };
-
   urlhunter = callPackage ../tools/security/urlhunter { };
 
   urlwatch = callPackage ../tools/networking/urlwatch { };
@@ -14336,8 +14225,6 @@ with pkgs;
 
   zpool-auto-expand-partitions = callPackage ../tools/filesystems/zpool-auto-expand-partitions { };
 
-  zile = callPackage ../applications/editors/zile { };
-
   zinnia = callPackage ../tools/inputmethods/zinnia { };
   tegaki-zinnia-japanese = callPackage ../tools/inputmethods/tegaki-zinnia-japanese { };
 
@@ -14595,14 +14482,8 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) Security SystemConfiguration;
   };
 
-  as31 = callPackage ../development/compilers/as31 { };
-
-  asl = callPackage ../development/compilers/asl { };
-
   aspectj = callPackage ../development/compilers/aspectj { };
 
-  atasm = callPackage ../development/compilers/atasm { };
-
   ats = callPackage ../development/compilers/ats { };
   ats2 = callPackage ../development/compilers/ats2 { };
 
@@ -14658,8 +14539,6 @@ with pkgs;
     chicken
     egg2nix;
 
-  cc65 = callPackage ../development/compilers/cc65 { };
-
   cdb = callPackage ../development/tools/database/cdb {
     stdenv = gccStdenv;
   };
@@ -15096,8 +14975,6 @@ with pkgs;
     gprbuild
     gnatprove;
 
-  gnu-smalltalk = callPackage ../development/compilers/gnu-smalltalk { };
-
   gccgo = wrapCC (gcc.cc.override {
     name = "gccgo";
     langCC = true; #required for go.
@@ -15347,8 +15224,6 @@ with pkgs;
 
   intel-graphics-compiler = callPackage ../development/compilers/intel-graphics-compiler { };
 
-  intercal = callPackage ../development/compilers/intercal { };
-
   irony-server = callPackage ../development/tools/irony-server {
     # The repository of irony to use -- must match the version of the employed emacs
     # package.  Wishing we could merge it into one irony package, to avoid this issue,
@@ -15633,8 +15508,6 @@ with pkgs;
 
   manticore = callPackage ../development/compilers/manticore { };
 
-  marst = callPackage ../development/compilers/marst { };
-
   mercury = callPackage ../development/compilers/mercury {
     jdk_headless = openjdk8_headless; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
@@ -15779,8 +15652,6 @@ with pkgs;
 
   passerine = callPackage ../development/compilers/passerine { };
 
-  pforth = callPackage ../development/compilers/pforth { };
-
   picat = callPackage ../development/compilers/picat { };
 
   ponyc = callPackage ../development/compilers/ponyc {
@@ -16518,8 +16389,6 @@ with pkgs;
 
   ivy = callPackage ../development/interpreters/ivy { };
 
-  j = callPackage ../development/interpreters/j { };
-
   jacinda = haskell.lib.compose.justStaticExecutables haskellPackages.jacinda;
 
   janet = callPackage ../development/interpreters/janet { };
@@ -16547,8 +16416,6 @@ with pkgs;
   lambda-lisp = callPackage ../development/interpreters/lambda-lisp { };
   lambda-lisp-blc = lambda-lisp;
 
-  lolcode = callPackage ../development/interpreters/lolcode { };
-
   love_0_10 = callPackage ../development/interpreters/love/0.10.nix { };
   love_11 = callPackage ../development/interpreters/love/11.nix { };
   love = love_11;
@@ -16973,8 +16840,6 @@ with pkgs;
 
   yaegi = callPackage ../development/interpreters/yaegi { };
 
-  yex-lang = callPackage ../development/interpreters/yex-lang { };
-
   ### DEVELOPMENT / MISC
 
   inherit (callPackages ../development/misc/h3 { }) h3_3 h3_4;
@@ -17269,8 +17134,6 @@ with pkgs;
 
   kt = callPackage ../tools/misc/kt { };
 
-  argbash = callPackage ../development/tools/misc/argbash { };
-
   arpa2cm = callPackage ../development/tools/build-managers/arpa2cm { };
 
   arpa2common = callPackage ../development/libraries/arpa2common { };
@@ -17323,8 +17186,6 @@ with pkgs;
   autoconf269 = callPackage ../development/tools/misc/autoconf/2.69.nix { };
   autoconf271 = callPackage ../development/tools/misc/autoconf/2.71.nix { };
 
-  acr  = callPackage ../development/tools/misc/acr { };
-
   autocutsel = callPackage ../tools/X11/autocutsel{ };
 
   automake = automake116x;
@@ -17558,8 +17419,6 @@ with pkgs;
 
   bpm-tools = callPackage ../tools/audio/bpm-tools { };
 
-  byacc = callPackage ../development/tools/parsing/byacc { };
-
   cadre = callPackage ../development/tools/cadre { };
 
   carto = callPackage ../development/tools/carto { };
@@ -17908,27 +17767,19 @@ with pkgs;
 
   evmdis = callPackage ../development/tools/analysis/evmdis { };
 
-  eweb = callPackage ../development/tools/literate-programming/eweb { };
-
   explain = callPackage ../development/tools/explain { };
 
   ezno = callPackage ../development/tools/misc/ezno { };
 
   func = callPackage ../applications/networking/cluster/func { };
 
-  funnelweb = callPackage ../development/tools/literate-programming/funnelweb { };
-
   license_finder = callPackage ../development/tools/license_finder { };
 
   license-scanner = callPackage ../development/tools/license-scanner { };
 
-  md-tangle = callPackage ../development/tools/literate-programming/md-tangle { };
-
   # NOTE: Override and set useIcon = false to use Awk instead of Icon.
   noweb = callPackage ../development/tools/literate-programming/noweb { };
 
-  nuweb = callPackage ../development/tools/literate-programming/nuweb { };
-
   eztrace = callPackage ../development/tools/profiling/EZTrace { };
 
   faas-cli = callPackage ../development/tools/faas-cli { };
@@ -18702,9 +18553,6 @@ with pkgs;
 
   rufo = callPackage ../development/tools/rufo { };
 
-  samurai = callPackage ../development/tools/build-managers/samurai { };
-
-  muon = callPackage ../development/tools/build-managers/muon { };
   muonStandalone = muon.override {
     embedSamurai = true;
     buildDocs = false;
@@ -19024,8 +18872,6 @@ with pkgs;
 
   uncrustify = callPackage ../development/tools/misc/uncrustify { };
 
-  universal-ctags = callPackage ../development/tools/misc/universal-ctags { };
-
   unused = callPackage ../development/tools/misc/unused { };
 
   vagrant = callPackage ../development/tools/vagrant { };
@@ -19149,8 +18995,6 @@ with pkgs;
 
   ytt = callPackage ../development/tools/ytt { };
 
-  zydis = callPackage ../development/libraries/zydis { };
-
   grabserial = callPackage ../development/tools/grabserial { };
 
   mypy = with python3Packages; toPythonApplication mypy;
@@ -20583,8 +20427,6 @@ with pkgs;
 
   hawknl = callPackage ../development/libraries/hawknl { };
 
-  hax11 = callPackage ../development/libraries/hax11 { };
-
   haxor-news = callPackage ../applications/misc/haxor-news { };
 
   hdt = callPackage ../misc/hdt { };
@@ -20979,8 +20821,6 @@ with pkgs;
 
   libargs = callPackage ../development/libraries/libargs { };
 
-  libarchive = callPackage ../development/libraries/libarchive { };
-
   libarchive-qt = libsForQt5.callPackage ../development/libraries/libarchive-qt { };
 
   libaribcaption = callPackage ../by-name/li/libaribcaption/package.nix {
@@ -20993,8 +20833,6 @@ with pkgs;
 
   libass = callPackage ../development/libraries/libass { };
 
-  libast = callPackage ../development/libraries/libast { };
-
   libassuan = callPackage ../development/libraries/libassuan { };
 
   libasyncns = callPackage ../development/libraries/libasyncns { };
@@ -21038,8 +20876,6 @@ with pkgs;
 
   libbs2b = callPackage ../development/libraries/audio/libbs2b { };
 
-  libcaca = callPackage ../development/libraries/libcaca { };
-
   libcacard = callPackage ../development/libraries/libcacard { };
 
   libcamera-qcam = callPackage ../by-name/li/libcamera/package.nix { withQcam = true; };
@@ -22023,8 +21859,6 @@ with pkgs;
 
   libtasn1 = callPackage ../development/libraries/libtasn1 { };
 
-  libtcod = callPackage ../development/libraries/libtcod { };
-
   libthai = callPackage ../development/libraries/libthai { };
 
   libthreadar = callPackage ../development/libraries/libthreadar { };
@@ -22058,8 +21892,6 @@ with pkgs;
 
   libtpms = callPackage ../tools/security/libtpms { };
 
-  libtap = callPackage ../development/libraries/libtap { };
-
   libtsm = callPackage ../development/libraries/libtsm { };
 
   libsv = callPackage ../development/libraries/libsv { };
@@ -22169,8 +22001,6 @@ with pkgs;
 
   libversion = callPackage ../development/libraries/libversion { };
 
-  libverto = callPackage ../development/libraries/libverto { };
-
   libvgm = callPackage ../development/libraries/libvgm {
     inherit (darwin.apple_sdk.frameworks) CoreAudio AudioToolbox;
   };
@@ -22397,8 +22227,6 @@ with pkgs;
 
   mdctags = callPackage ../development/tools/misc/mdctags { };
 
-  mdds = callPackage ../development/libraries/mdds { };
-
   mediastreamer = libsForQt5.callPackage ../development/libraries/mediastreamer { };
 
   mediastreamer-openh264 = callPackage ../development/libraries/mediastreamer/msopenh264.nix { };
@@ -22625,8 +22453,6 @@ with pkgs;
 
   nanodbc = callPackage ../development/libraries/nanodbc { };
 
-  nanoflann = callPackage ../development/libraries/nanoflann { };
-
   nanomsg = callPackage ../development/libraries/nanomsg { };
 
   nanosvg = callPackage ../development/libraries/nanosvg { };
@@ -22647,8 +22473,6 @@ with pkgs;
 
   notify-sharp = callPackage ../development/libraries/notify-sharp { };
 
-  notcurses = callPackage ../development/libraries/notcurses { };
-
   ncurses5 = ncurses.override {
     abiVersion = "5";
   };
@@ -22939,8 +22763,6 @@ with pkgs;
 
   p11-kit = callPackage ../development/libraries/p11-kit { };
 
-  paperkey = callPackage ../tools/security/paperkey { };
-
   parsero = callPackage ../tools/security/parsero { };
 
   pcaudiolib = callPackage ../development/libraries/pcaudiolib { };
@@ -23469,8 +23291,6 @@ with pkgs;
 
   shaq = callPackage ../tools/audio/shaq { };
 
-  slang = callPackage ../development/libraries/slang { };
-
   slibGuile = callPackage ../development/libraries/slib {
     scheme = guile;
   };
@@ -23635,8 +23455,6 @@ with pkgs;
 
   stb = callPackage ../development/libraries/stb { };
 
-  steghide = callPackage ../tools/graphics/steghide { };
-
   stegsolve = callPackage ../tools/graphics/stegsolve { };
 
   stxxl = callPackage ../development/libraries/stxxl { };
@@ -23701,8 +23519,6 @@ with pkgs;
 
   svxlink = libsForQt5.callPackage ../applications/radio/svxlink { };
 
-  biblesync = callPackage ../development/libraries/biblesync { };
-
   szip = callPackage ../development/libraries/szip { };
 
   t1lib = callPackage ../development/libraries/t1lib { };
@@ -23812,12 +23628,6 @@ with pkgs;
 
   kyotocabinet = callPackage ../development/libraries/kyotocabinet { };
 
-  tomlc99 = callPackage ../development/libraries/tomlc99 { };
-
-  tomlcpp = callPackage ../development/libraries/tomlcpp { };
-
-  toml11 = callPackage ../development/libraries/toml11 { };
-
   tomlplusplus = callPackage ../development/libraries/tomlplusplus { };
 
   tokyocabinet = callPackage ../development/libraries/tokyo-cabinet { };
@@ -23832,12 +23642,8 @@ with pkgs;
 
   tremor = callPackage ../development/libraries/tremor { };
 
-  triehash = callPackage ../tools/misc/triehash { };
-
   trillian = callPackage ../tools/misc/trillian { };
 
-  twolame = callPackage ../development/libraries/twolame { };
-
   udns = callPackage ../development/libraries/udns { };
 
   uid_wrapper = callPackage ../development/libraries/uid_wrapper { };
@@ -24211,10 +24017,6 @@ with pkgs;
 
   zix = callPackage ../development/libraries/audio/zix { };
 
-  zziplib = callPackage ../development/libraries/zziplib { };
-
-  glpng = callPackage ../development/libraries/glpng { };
-
   gsignond = callPackage ../development/libraries/gsignond {
     plugins = [];
   };
@@ -24818,8 +24620,6 @@ with pkgs;
 
   go-cqhttp = callPackage ../servers/go-cqhttp { };
 
-  gofish = callPackage ../servers/gopher/gofish { };
-
   grafana = callPackage ../servers/monitoring/grafana { };
   grafanaPlugins = callPackages ../servers/monitoring/grafana/plugins { };
 
@@ -25942,8 +25742,6 @@ with pkgs;
 
   atop = callPackage ../os-specific/linux/atop { };
 
-  audit = callPackage ../os-specific/linux/audit { };
-
   ath9k-htc-blobless-firmware = callPackage ../os-specific/linux/firmware/ath9k { };
   ath9k-htc-blobless-firmware-unstable =
     callPackage ../os-specific/linux/firmware/ath9k { enableUnstable = true; };
@@ -27407,8 +27205,6 @@ with pkgs;
 
   comic-mono = callPackage ../data/fonts/comic-mono { };
 
-  comic-neue = callPackage ../data/fonts/comic-neue { };
-
   comic-relief = callPackage ../data/fonts/comic-relief { };
 
   comixcursors = callPackage ../data/icons/comixcursors { };
@@ -27993,8 +27789,6 @@ with pkgs;
 
   numix-sx-gtk-theme = callPackage ../data/themes/numix-sx { };
 
-  office-code-pro = callPackage ../data/fonts/office-code-pro { };
-
   _0xproto = callPackage ../data/fonts/0xproto { };
 
   oldstandard = callPackage ../data/fonts/oldstandard { };
@@ -29103,8 +28897,6 @@ with pkgs;
 
   clp = callPackage ../applications/science/math/clp { };
 
-  cmatrix = callPackage ../applications/misc/cmatrix { };
-
   pokemon-colorscripts-mac = callPackage ../applications/misc/pokemon-colorscripts-mac { };
 
   cmctl = callPackage ../applications/networking/cluster/cmctl { };
@@ -29397,8 +29189,6 @@ with pkgs;
 
   dvd-slideshow = callPackage ../applications/video/dvd-slideshow { };
 
-  dvdstyler = callPackage ../applications/video/dvdstyler { };
-
   dyff = callPackage ../development/tools/dyff { };
 
   dwl = callPackage ../by-name/dw/dwl/package.nix {
@@ -29443,8 +29233,6 @@ with pkgs;
 
   ecs-agent = callPackage ../applications/virtualization/ecs-agent { };
 
-  edlin = callPackage ../applications/editors/edlin { };
-
   oed = callPackage ../applications/editors/oed { };
 
   electron-cash = libsForQt5.callPackage ../applications/misc/electron-cash { };
@@ -29465,8 +29253,6 @@ with pkgs;
 
   elvis = callPackage ../applications/editors/elvis { };
 
-  em = callPackage ../applications/editors/em { };
-
   inherit (recurseIntoAttrs (callPackage ../applications/editors/emacs { }))
     emacs28
     emacs28-gtk2
@@ -29706,8 +29492,6 @@ with pkgs;
 
   foliate = callPackage ../applications/office/foliate { };
 
-  fondo = callPackage ../applications/graphics/fondo { };
-
   font-manager = callPackage ../by-name/fo/font-manager/package.nix {
     libsoup = libsoup_3;
     webkitgtk = webkitgtk_6_0;
@@ -30061,10 +29845,6 @@ with pkgs;
 
   floorp = wrapFirefox floorp-unwrapped { };
 
-  fluxbox = callPackage ../applications/window-managers/fluxbox { };
-
-  hackedbox = callPackage ../applications/window-managers/hackedbox { };
-
   fomp = callPackage ../applications/audio/fomp { };
 
   formatter = callPackage ../applications/misc/formatter { };
@@ -30157,8 +29937,6 @@ with pkgs;
 
   gmrun = callPackage ../applications/misc/gmrun { };
 
-  gnucash = callPackage ../applications/office/gnucash { };
-
   goffice = callPackage ../development/libraries/goffice { };
 
   gtkterm = callPackage ../tools/misc/gtkterm { };
@@ -30305,8 +30083,6 @@ with pkgs;
 
   q4wine = libsForQt5.callPackage ../applications/misc/q4wine { };
 
-  qrcodegen = callPackage ../development/libraries/qrcodegen { };
-
   qrencode = callPackage ../development/libraries/qrencode {
     inherit (darwin) libobjc;
   };
@@ -30525,8 +30301,6 @@ with pkgs;
 
   levant = callPackage ../applications/networking/cluster/levant { };
 
-  lwm = callPackage ../applications/window-managers/lwm { };
-
   marker = callPackage ../applications/editors/marker { };
 
   matcha-rss-digest = callPackage ../applications/misc/matcha-rss-digest { };
@@ -30636,8 +30410,6 @@ with pkgs;
 
   remontoire = callPackage ../applications/misc/remontoire { };
 
-  rootbar = callPackage ../applications/misc/rootbar { };
-
   waycorner = callPackage ../applications/misc/waycorner { };
 
   wayshot = callPackage ../tools/misc/wayshot { };
@@ -30879,8 +30651,6 @@ with pkgs;
 
   fish-irssi = callPackage ../applications/networking/irc/irssi/fish { };
 
-  kirc = callPackage ../applications/networking/irc/kirc { };
-
   ir.lv2 = callPackage ../applications/audio/ir.lv2 { };
 
   istioctl = callPackage ../applications/networking/cluster/istioctl { };
@@ -30945,8 +30715,6 @@ with pkgs;
 
   jitsi = callPackage ../applications/networking/instant-messengers/jitsi { };
 
-  joe = callPackage ../applications/editors/joe { };
-
   johnny = callPackage ../applications/misc/johnny { };
 
   js8call = qt5.callPackage ../applications/radio/js8call { };
@@ -31509,8 +31277,6 @@ with pkgs;
 
   mbrola-voices = callPackage ../applications/audio/mbrola/voices.nix { };
 
-  mcpp = callPackage ../development/compilers/mcpp { };
-
   mda_lv2 = callPackage ../applications/audio/mda-lv2 { };
 
   mdzk = callPackage ../applications/misc/mdzk {
@@ -31850,8 +31616,6 @@ with pkgs;
 
   mu-repo = python3Packages.callPackage ../applications/misc/mu-repo { };
 
-  multimarkdown = callPackage ../tools/typesetting/multimarkdown { };
-
   multimon-ng = callPackage ../applications/radio/multimon-ng { };
 
   murmur = (callPackages ../applications/networking/mumble {
@@ -32025,8 +31789,6 @@ with pkgs;
     i3Support = true;
   };
 
-  yambar = callPackage ../applications/misc/yambar { };
-
   yambar-hyprland-wses = callPackage ../applications/misc/yambar-hyprland-wses { };
 
   polyphone = qt6.callPackage ../applications/audio/polyphone { };
@@ -32082,20 +31844,12 @@ with pkgs;
 
   typora = callPackage ../applications/editors/typora { };
 
-  taxi = callPackage ../applications/networking/ftp/taxi { };
-
   taxi-cli = with python3Packages; toPythonApplication taxi;
 
   tcping-go = callPackage ../applications/networking/tcping-go { };
 
-  librep = callPackage ../development/libraries/librep { };
-
-  rep-gtk = callPackage ../development/libraries/rep-gtk { };
-
   reproc = callPackage ../development/libraries/reproc { };
 
-  sawfish = callPackage ../applications/window-managers/sawfish { };
-
   sc68 = callPackage ../applications/audio/sc68 { };
 
   sidplayfp = callPackage ../applications/audio/sidplayfp { };
@@ -32213,8 +31967,6 @@ with pkgs;
 
   notmuch-mailmover = callPackage ../applications/networking/mailreaders/notmuch/notmuch-mailmover.nix { };
 
-  notejot = callPackage ../applications/misc/notejot { };
-
   notmuch-mutt = callPackage ../applications/networking/mailreaders/notmuch/mutt.nix { };
 
   muchsync = callPackage ../applications/networking/mailreaders/notmuch/muchsync.nix { };
@@ -32562,8 +32314,6 @@ with pkgs;
 
   plugin-torture = callPackage ../applications/audio/plugin-torture { };
 
-  poke = callPackage ../applications/editors/poke { };
-
   pokefinder = qt6Packages.callPackage ../tools/games/pokefinder { };
 
   pokemonsay = callPackage ../tools/misc/pokemonsay { };
@@ -32993,10 +32743,6 @@ with pkgs;
 
   uade = callPackage ../applications/audio/uade { };
 
-  udevil = callPackage ../applications/misc/udevil { };
-
-  udiskie = callPackage ../applications/misc/udiskie { };
-
   sacc = callPackage ../applications/networking/gopher/sacc { };
 
   savvycan = libsForQt5.callPackage ../applications/networking/sniffers/savvycan {};
@@ -33453,8 +33199,6 @@ with pkgs;
 
   taskell = haskell.lib.compose.justStaticExecutables haskellPackages.taskell;
 
-  tap-plugins = callPackage ../applications/audio/tap-plugins { };
-
   taskjuggler = callPackage ../applications/misc/taskjuggler { };
 
   tabula-java = callPackage ../applications/misc/tabula-java { };
@@ -33523,8 +33267,6 @@ with pkgs;
 
   texturepacker = qt6.callPackage ../applications/graphics/texturepacker { };
 
-  tty-solitaire = callPackage ../applications/misc/tty-solitaire { };
-
   termtosvg = callPackage ../tools/misc/termtosvg { };
 
   tessen = callPackage ../tools/security/tessen { };
@@ -33772,8 +33514,6 @@ with pkgs;
 
   tests-stdenv-gcc-stageCompare = callPackage ../test/stdenv/gcc-stageCompare.nix { };
 
-  lavalauncher = callPackage ../applications/misc/lavalauncher { };
-
   t-rec = callPackage ../misc/t-rec {
     inherit (darwin.apple_sdk.frameworks) Foundation;
   };
@@ -33934,8 +33674,6 @@ with pkgs;
 
   gnvim = callPackage ../applications/editors/neovim/gnvim/wrapper.nix { };
 
-  viw = callPackage ../applications/editors/viw { };
-
   virter = callPackage ../applications/virtualization/virter { };
 
   virt-viewer = callPackage ../applications/virtualization/virt-viewer { };
@@ -34290,9 +34028,6 @@ with pkgs;
     wxGTK = wxGTK32;
   };
 
-  xa = callPackage ../development/compilers/xa/xa.nix { };
-  dxa = callPackage ../development/compilers/xa/dxa.nix { };
-
   x11basic = callPackage ../development/compilers/x11basic {
     autoconf = buildPackages.autoconf269;
   };
@@ -34426,8 +34161,6 @@ with pkgs;
     inherit (gnome2) libglade GConf;
   };
 
-  xiphos = callPackage ../applications/misc/xiphos { };
-
   xournal = callPackage ../applications/graphics/xournal {
     inherit (gnome2) libgnomecanvas;
   };
@@ -34939,8 +34672,6 @@ with pkgs;
 
   ### GAMES
 
-  _1oom = callPackage ../games/1oom { };
-
   _2048-cli = _2048-cli-terminal;
   _2048-cli-curses = callPackage ../games/2048-cli { ui = "curses"; };
   _2048-cli-terminal = callPackage ../games/2048-cli { ui = "terminal"; };
@@ -34951,8 +34682,6 @@ with pkgs;
 
   _90secondportraits = callPackage ../games/90secondportraits { love = love_0_10; };
 
-  ace-of-penguins = callPackage ../games/ace-of-penguins { };
-
   among-sus = callPackage ../games/among-sus { };
 
   antsimulator = callPackage ../games/antsimulator { };
@@ -35201,10 +34930,6 @@ with pkgs;
 
   braincurses = callPackage ../games/braincurses { };
 
-  brogue = callPackage ../games/brogue { };
-
-  brogue-ce = callPackage ../games/brogue-ce { };
-
   brutalmaze = callPackage ../games/brutalmaze { };
 
   bsdgames = callPackage ../games/bsdgames { };
@@ -35247,8 +34972,6 @@ with pkgs;
     });
   };
 
-  chromium-bsu = callPackage ../games/chromium-bsu { };
-
   clonehero = callPackage ../games/clonehero { };
 
   vintagestory = callPackage ../games/vintagestory { };
@@ -36243,8 +35966,6 @@ with pkgs;
 
   zeroad = zeroadPackages.zeroad;
 
-  _0verkill = callPackage ../games/0verkill { };
-
   _7kaa = callPackage ../games/7kaa { };
 
   hhexen = callPackage ../games/hhexen { };
@@ -36396,8 +36117,6 @@ with pkgs;
 
   avogadro2 = libsForQt5.callPackage ../applications/science/chemistry/avogadro2 { };
 
-  chemtool = callPackage ../applications/science/chemistry/chemtool { };
-
   cp2k = callPackage ../applications/science/chemistry/cp2k { };
 
   d-seams = callPackage ../applications/science/chemistry/d-seams { };
@@ -36449,8 +36168,6 @@ with pkgs;
 
   ### SCIENCE/GEOMETRY
 
-  antiprism = callPackage ../applications/science/geometry/antiprism { };
-
   gama = callPackage ../applications/science/geometry/gama { };
 
   tetgen = callPackage ../applications/science/geometry/tetgen { }; # AGPL3+
@@ -36743,8 +36460,6 @@ with pkgs;
 
   ### SCIENCE/MATH
 
-  _4ti2  = callPackage ../applications/science/math/4ti2 { };
-
   almonds = callPackage ../applications/science/math/almonds { };
 
   adolc = callPackage ../applications/science/math/adolc { };
@@ -37438,8 +37153,6 @@ with pkgs;
 
   caffeine-ng = callPackage ../tools/X11/caffeine-ng { };
 
-  dap = callPackage ../applications/science/math/dap { };
-
   ecm = callPackage ../applications/science/math/ecm { };
 
   eukleides = callPackage ../applications/science/math/eukleides { };
@@ -37859,12 +37572,8 @@ with pkgs;
 
   electricsheep = callPackage ../misc/screensavers/electricsheep { };
 
-  aaphoto = callPackage ../tools/graphics/aaphoto { };
-
   aapt = callPackage ../development/tools/aapt { };
 
-  flam3 = callPackage ../tools/graphics/flam3 { };
-
   glee = callPackage ../tools/graphics/glee { };
 
   faust = res.faust2;
@@ -38547,8 +38256,6 @@ with pkgs;
 
   runitor = callPackage ../tools/system/runitor { };
 
-  refind = callPackage ../tools/bootloaders/refind { };
-
   refmt = callPackage ../development/tools/refmt { };
 
   spectra = callPackage ../development/libraries/spectra { };
@@ -38903,8 +38610,6 @@ with pkgs;
     llvmPackages = llvmPackages_12;
   };
 
-  yabasic = callPackage ../development/interpreters/yabasic { };
-
   wasm-pack = callPackage ../development/tools/wasm-pack { };
 
   wasynth = callPackage ../development/tools/wasynth { };
@@ -38967,8 +38672,6 @@ with pkgs;
 
   wishbone-tool = callPackage ../development/tools/misc/wishbone-tool { };
 
-  with-shell = callPackage ../applications/misc/with-shell { };
-
   wmutils-core = callPackage ../tools/X11/wmutils-core { };
 
   wmutils-libwm = callPackage ../tools/X11/wmutils-libwm { };
@@ -39111,8 +38814,6 @@ with pkgs;
 
   zxcvbn-c = callPackage ../development/libraries/zxcvbn-c { };
 
-  zxing-cpp = callPackage ../development/libraries/zxing-cpp { };
-
   bullet = callPackage ../development/libraries/bullet {
     inherit (darwin.apple_sdk.frameworks) Cocoa OpenGL;
   };
@@ -39356,8 +39057,6 @@ with pkgs;
 
   bemenu = callPackage ../applications/misc/bemenu { };
 
-  _9menu = callPackage ../applications/misc/9menu { };
-
   dapper = callPackage ../development/tools/dapper { };
 
   k3d = callPackage ../applications/networking/cluster/k3d { };
diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix
index f789cd32996b..3bcb357458f8 100644
--- a/pkgs/top-level/python-aliases.nix
+++ b/pkgs/top-level/python-aliases.nix
@@ -483,6 +483,7 @@ mapAliases ({
   pytest-pep8 = pytestpep8; # added 2021-01-04
   pytest-pep257 = throw "pytest-pep257 was removed, as the pep257 package was migrated into pycodestyle"; # added 2022-04-12
   pytest-pythonpath = throw "pytest-pythonpath is obsolete as of pytest 7.0.0 and has been removed"; # added 2022-03-09
+  pytest-runner = throw "pytest-runner has been removed as it uses deprecated features of setuptools and is deprecated by upstream"; # added 2024-09-15
   pytest-sanic = throw "pytest-sanic has been removed because it is unmaintained and broken"; # added 2023-06-22
   pytestpep8 = throw "pytestpep8 was removed because it is abandoned and no longer compatible with pytest v6.0"; # added 2020-12-10
   pytestquickcheck = pytest-quickcheck; # added 2021-07-20
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 8c42c154b1ae..0ebfafb06e41 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -12474,8 +12474,6 @@ self: super: with self; {
 
   pytest-responses = callPackage ../development/python-modules/pytest-responses { };
 
-  pytest-runner = callPackage ../development/python-modules/pytest-runner { };
-
   pytest-server-fixtures = callPackage ../development/python-modules/pytest-server-fixtures { };
 
   pytest-services = callPackage ../development/python-modules/pytest-services { };
diff --git a/pkgs/top-level/qt5-packages.nix b/pkgs/top-level/qt5-packages.nix
index 2e746d5c7d5d..b0091a16f3da 100644
--- a/pkgs/top-level/qt5-packages.nix
+++ b/pkgs/top-level/qt5-packages.nix
@@ -40,7 +40,6 @@ makeScopeWithSplicing' {
     attrs = {
       inherit libsForQt5;
       inherit (pkgs) config lib fetchurl;
-      gconf = pkgs.gnome2.GConf;
       inherit (pkgs) gsettings-desktop-schemas;
     };
   in (lib.makeOverridable mkPlasma5 attrs);