diff --git a/ci/default.nix b/ci/default.nix
index 0aeb2356e9ae..da6e3f877e3b 100644
--- a/ci/default.nix
+++ b/ci/default.nix
@@ -17,7 +17,12 @@ let
     else
       nixpkgs;
 
-  pkgs = import nixpkgs' { inherit system; };
+  pkgs = import nixpkgs' {
+    inherit system;
+    # Nixpkgs generally — and CI specifically — do not use aliases,
+    # because we want to ensure they are not load-bearing.
+    allowAliases = false;
+  };
 
   fmt =
     let
@@ -60,10 +65,12 @@ let
 
         programs.keep-sorted.enable = true;
 
-        # This uses nixfmt underneath,
-        # the default formatter for Nix code.
+        # This uses nixfmt underneath, the default formatter for Nix code.
         # See https://github.com/NixOS/nixfmt
-        programs.nixfmt.enable = true;
+        programs.nixfmt = {
+          enable = true;
+          package = pkgs.nixfmt;
+        };
 
         programs.yamlfmt = {
           enable = true;
@@ -134,7 +141,9 @@ rec {
   manual-nixos = (import ../nixos/release.nix { }).manual.${system} or null;
   manual-nixpkgs = (import ../doc { inherit pkgs; });
   manual-nixpkgs-tests = (import ../doc { inherit pkgs; }).tests;
-  nixpkgs-vet = pkgs.callPackage ./nixpkgs-vet.nix { };
+  nixpkgs-vet = pkgs.callPackage ./nixpkgs-vet.nix {
+    nix = pkgs.nixVersions.latest;
+  };
   parse = pkgs.lib.recurseIntoAttrs {
     latest = pkgs.callPackage ./parse.nix { nix = pkgs.nixVersions.latest; };
     lix = pkgs.callPackage ./parse.nix { nix = pkgs.lix; };
diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index a57893dbd55b..b10c92acaa98 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -7275,6 +7275,12 @@
     github = "eigengrau";
     githubId = 4939947;
   };
+  eihqnh = {
+    email = "eihqnh@outlook.com";
+    github = "eihqnh";
+    githubId = 40905037;
+    name = "eihqnh";
+  };
   eikek = {
     email = "eike.kettner@posteo.de";
     github = "eikek";
@@ -20958,12 +20964,6 @@
     githubId = 2141853;
     name = "Bang Lee";
   };
-  qwqawawow = {
-    email = "eihqnh@outlook.com";
-    github = "qwqawawow";
-    githubId = 40905037;
-    name = "qwqawawow";
-  };
   qxrein = {
     email = "mnv07@proton.me";
     github = "qxrein";
diff --git a/nixos/modules/services/networking/prosody.nix b/nixos/modules/services/networking/prosody.nix
index 198d99501f2c..cf973dd242a5 100644
--- a/nixos/modules/services/networking/prosody.nix
+++ b/nixos/modules/services/networking/prosody.nix
@@ -880,7 +880,11 @@ in
       extraConfig = mkOption {
         type = types.lines;
         default = "";
-        description = "Additional prosody configuration";
+        description = ''
+          Additional prosody configuration
+
+          The generated file is processed by `envsubst` to allow secrets to be passed securely via environment variables.
+        '';
       };
 
       log = mkOption {
@@ -974,13 +978,19 @@ in
       wants = [ "network-online.target" ];
       wantedBy = [ "multi-user.target" ];
       restartTriggers = [ config.environment.etc."prosody/prosody.cfg.lua".source ];
+      preStart = ''
+        ${pkgs.envsubst}/bin/envsubst -i ${
+          config.environment.etc."prosody/prosody.cfg.lua".source
+        } -o /run/prosody/prosody.cfg.lua
+      '';
       serviceConfig = mkMerge [
         {
           User = cfg.user;
           Group = cfg.group;
           Type = "simple";
-          RuntimeDirectory = [ "prosody" ];
+          RuntimeDirectory = "prosody";
           PIDFile = "/run/prosody/prosody.pid";
+          Environment = "PROSODY_CONFIG=/run/prosody/prosody.cfg.lua";
           ExecStart = "${lib.getExe cfg.package} -F";
           ExecReload = "${pkgs.coreutils}/bin/kill -HUP $MAINPID";
           Restart = "on-abnormal";
diff --git a/pkgs/applications/misc/zettlr/default.nix b/pkgs/applications/misc/zettlr/default.nix
deleted file mode 100644
index 1fdbe190ce82..000000000000
--- a/pkgs/applications/misc/zettlr/default.nix
+++ /dev/null
@@ -1,8 +0,0 @@
-{ callPackage }:
-
-builtins.mapAttrs (pname: attrs: callPackage ./generic.nix (attrs // { inherit pname; })) {
-  zettlr = {
-    version = "3.4.4";
-    hash = "sha256-ApgmHl9WoAmWl03tqv01D0W8orja25f7KZUFLhlZloQ=";
-  };
-}
diff --git a/pkgs/by-name/_1/_1password-gui/sources.json b/pkgs/by-name/_1/_1password-gui/sources.json
index f506b03a5beb..1e77e1f21a86 100644
--- a/pkgs/by-name/_1/_1password-gui/sources.json
+++ b/pkgs/by-name/_1/_1password-gui/sources.json
@@ -1,56 +1,56 @@
 {
   "stable": {
     "linux": {
-      "version": "8.11.4",
+      "version": "8.11.6",
       "sources": {
         "x86_64": {
-          "url": "https://downloads.1password.com/linux/tar/stable/x86_64/1password-8.11.4.x64.tar.gz",
-          "hash": "sha256-s/CV1hA8j3ivWEmKfwMd6Hh74BY86C0MZLDwjm6ROd4="
+          "url": "https://downloads.1password.com/linux/tar/stable/x86_64/1password-8.11.6.x64.tar.gz",
+          "hash": "sha256-OjyJDesweUhLHuBeLCEvNOloDZO8/D6Z1FquLyapQ4Q="
         },
         "aarch64": {
-          "url": "https://downloads.1password.com/linux/tar/stable/aarch64/1password-8.11.4.arm64.tar.gz",
-          "hash": "sha256-qljiVRVO0HlteI5oRQPLb6+JL282CwcbRydANUmNcRM="
+          "url": "https://downloads.1password.com/linux/tar/stable/aarch64/1password-8.11.6.arm64.tar.gz",
+          "hash": "sha256-sspmxX6xeVHvEww4D41PZTM2YftbILx06aMuDbAay74="
         }
       }
     },
     "darwin": {
-      "version": "8.11.4",
+      "version": "8.11.6",
       "sources": {
         "x86_64": {
-          "url": "https://downloads.1password.com/mac/1Password-8.11.4-x86_64.zip",
-          "hash": "sha256-kv+TSoZcoCkL1Gr0dwgqtYK532wEnergVAwCMCv44/A="
+          "url": "https://downloads.1password.com/mac/1Password-8.11.6-x86_64.zip",
+          "hash": "sha256-HMwb22/4Dw3M3B1nrdURSQzMGAZxsVG6t8E+MUmRmjg="
         },
         "aarch64": {
-          "url": "https://downloads.1password.com/mac/1Password-8.11.4-aarch64.zip",
-          "hash": "sha256-AhWPz/cwhBwSozZx6WrDPvCj73OIvBxXlsimM+FDFlA="
+          "url": "https://downloads.1password.com/mac/1Password-8.11.6-aarch64.zip",
+          "hash": "sha256-SrB4tUk2GroUOptdQlJsC9tFssYXduyLR1TqH7aU2N4="
         }
       }
     }
   },
   "beta": {
     "linux": {
-      "version": "8.11.4-21.BETA",
+      "version": "8.11.8-32.BETA",
       "sources": {
         "x86_64": {
-          "url": "https://downloads.1password.com/linux/tar/beta/x86_64/1password-8.11.4-21.BETA.x64.tar.gz",
-          "hash": "sha256-HWPeTCtjHH8vngDX0+tGbiDMj1FoW8a4RCu34RqJXmI="
+          "url": "https://downloads.1password.com/linux/tar/beta/x86_64/1password-8.11.8-32.BETA.x64.tar.gz",
+          "hash": "sha256-FlJ7uXtqavcOUs/DRGCMR0ImX9mlQBYGxFzM45DByBg="
         },
         "aarch64": {
-          "url": "https://downloads.1password.com/linux/tar/beta/aarch64/1password-8.11.4-21.BETA.arm64.tar.gz",
-          "hash": "sha256-yPjzweuJPvvOkJcIElaAogzBpWPvYch6DQarRoaZojc="
+          "url": "https://downloads.1password.com/linux/tar/beta/aarch64/1password-8.11.8-32.BETA.arm64.tar.gz",
+          "hash": "sha256-Dqy9keq6aRrFp2zKGOpV9kmI4CZQFZpf8ey9n9OKy8A="
         }
       }
     },
     "darwin": {
-      "version": "8.11.4-21.BETA",
+      "version": "8.11.8-32.BETA",
       "sources": {
         "x86_64": {
-          "url": "https://downloads.1password.com/mac/1Password-8.11.4-21.BETA-x86_64.zip",
-          "hash": "sha256-FozwWYQCrqWbfw9qaPRLbaUVWa5hTwG3NHjtZc4smdk="
+          "url": "https://downloads.1password.com/mac/1Password-8.11.8-32.BETA-x86_64.zip",
+          "hash": "sha256-OEl6maJ5bDW9ySLYXWnHUNYY48dtrjxZppRMCUzHrq8="
         },
         "aarch64": {
-          "url": "https://downloads.1password.com/mac/1Password-8.11.4-21.BETA-aarch64.zip",
-          "hash": "sha256-0eXtLqknEPG+G+mxa7QYWkUVPu13/KAdkOb9fklZIqg="
+          "url": "https://downloads.1password.com/mac/1Password-8.11.8-32.BETA-aarch64.zip",
+          "hash": "sha256-cNKC+JIsPHMk9h5pBcuh6huLWd7aqt7AdB4ixQ99oeE="
         }
       }
     }
diff --git a/pkgs/development/libraries/bullet/gwen-narrowing.patch b/pkgs/by-name/bu/bullet-roboschool/gwen-narrowing.patch
similarity index 100%
rename from pkgs/development/libraries/bullet/gwen-narrowing.patch
rename to pkgs/by-name/bu/bullet-roboschool/gwen-narrowing.patch
diff --git a/pkgs/development/libraries/bullet/roboschool-fork.nix b/pkgs/by-name/bu/bullet-roboschool/package.nix
similarity index 100%
rename from pkgs/development/libraries/bullet/roboschool-fork.nix
rename to pkgs/by-name/bu/bullet-roboschool/package.nix
diff --git a/pkgs/development/libraries/bullet/default.nix b/pkgs/by-name/bu/bullet/package.nix
similarity index 100%
rename from pkgs/development/libraries/bullet/default.nix
rename to pkgs/by-name/bu/bullet/package.nix
diff --git a/pkgs/tools/compression/bzip3/default.nix b/pkgs/by-name/bz/bzip3/package.nix
similarity index 77%
rename from pkgs/tools/compression/bzip3/default.nix
rename to pkgs/by-name/bz/bzip3/package.nix
index 9447ee19fb5b..e70cb63a5a95 100644
--- a/pkgs/tools/compression/bzip3/default.nix
+++ b/pkgs/by-name/bz/bzip3/package.nix
@@ -9,7 +9,7 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "bzip3";
-  version = "1.5.2";
+  version = "1.5.3";
 
   outputs = [
     "bin"
@@ -18,10 +18,10 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   src = fetchFromGitHub {
-    owner = "kspalaiologos";
+    owner = "iczelia";
     repo = "bzip3";
-    rev = finalAttrs.version;
-    hash = "sha256-mu95ZYkD0isDuHdHcU4zhWxCTlaYXoM85j76IGwVAak=";
+    tag = finalAttrs.version;
+    hash = "sha256-SOouMUctxsAJdkt84rJBaCbK23GKmXRH9nVgGdDodsk=";
   };
 
   postPatch = ''
@@ -46,8 +46,8 @@ stdenv.mkDerivation (finalAttrs: {
 
   meta = {
     description = "Better and stronger spiritual successor to BZip2";
-    homepage = "https://github.com/kspalaiologos/bzip3";
-    changelog = "https://github.com/kspalaiologos/bzip3/blob/${finalAttrs.src.rev}/NEWS";
+    homepage = "https://github.com/iczelia/bzip3";
+    changelog = "https://github.com/iczelia/bzip3/blob/${finalAttrs.src.tag}/NEWS";
     license = lib.licenses.lgpl3Plus;
     maintainers = with lib.maintainers; [ dotlambda ];
     pkgConfigModules = [ "bzip3" ];
diff --git a/pkgs/by-name/ca/cabinpkg/package.nix b/pkgs/by-name/ca/cabinpkg/package.nix
index a4604868d6f5..31d35851dcf8 100644
--- a/pkgs/by-name/ca/cabinpkg/package.nix
+++ b/pkgs/by-name/ca/cabinpkg/package.nix
@@ -70,7 +70,7 @@ stdenv.mkDerivation rec {
     homepage = "https://cabinpkg.com";
     description = "Package manager and build system for C++";
     license = lib.licenses.asl20;
-    maintainers = [ lib.maintainers.qwqawawow ];
+    maintainers = [ lib.maintainers.eihqnh ];
     platforms = lib.platforms.unix;
     mainProgram = "cabin";
   };
diff --git a/pkgs/by-name/ca/cargo-seek/package.nix b/pkgs/by-name/ca/cargo-seek/package.nix
index 8d665635f2ea..cc44c9330682 100644
--- a/pkgs/by-name/ca/cargo-seek/package.nix
+++ b/pkgs/by-name/ca/cargo-seek/package.nix
@@ -41,7 +41,7 @@ rustPlatform.buildRustPackage (finalAttrs: {
     homepage = "https://github.com/tareqimbasher/cargo-seek";
     changelog = "https://github.com/tareqimbasher/cargo-seek/releases/tag/v${finalAttrs.version}";
     license = lib.licenses.mit;
-    maintainers = with lib.maintainers; [ qwqawawow ];
+    maintainers = with lib.maintainers; [ eihqnh ];
     mainProgram = "cargo-seek";
   };
 })
diff --git a/pkgs/by-name/cl/claude-code/package-lock.json b/pkgs/by-name/cl/claude-code/package-lock.json
index 6baa91162a87..08c2e439a644 100644
--- a/pkgs/by-name/cl/claude-code/package-lock.json
+++ b/pkgs/by-name/cl/claude-code/package-lock.json
@@ -6,13 +6,13 @@
   "packages": {
     "": {
       "dependencies": {
-        "@anthropic-ai/claude-code": "^1.0.85"
+        "@anthropic-ai/claude-code": "^1.0.86"
       }
     },
     "node_modules/@anthropic-ai/claude-code": {
-      "version": "1.0.85",
-      "resolved": "https://registry.npmjs.org/@anthropic-ai/claude-code/-/claude-code-1.0.85.tgz",
-      "integrity": "sha512-rvLGGSnHQLJI3dP7C/d3Or5LQvgDEae5wurMG4Fs9ourzt+k8YA6WAHeuJmSUq7o7Z2fZTaojcM3VOLzUBEl7w==",
+      "version": "1.0.86",
+      "resolved": "https://registry.npmjs.org/@anthropic-ai/claude-code/-/claude-code-1.0.86.tgz",
+      "integrity": "sha512-js1h6JUnFJ1dHvFPBiCxwFChaWjh28XOFamrwebmhOIUBVhQZwMfDJYsNfRyv0qEwpxKxYedvK4nv4WqMCwu9Q==",
       "license": "SEE LICENSE IN README.md",
       "bin": {
         "claude": "cli.js"
diff --git a/pkgs/by-name/cl/claude-code/package.nix b/pkgs/by-name/cl/claude-code/package.nix
index 14eba606feab..e36d28b5f9a9 100644
--- a/pkgs/by-name/cl/claude-code/package.nix
+++ b/pkgs/by-name/cl/claude-code/package.nix
@@ -7,16 +7,16 @@
 
 buildNpmPackage rec {
   pname = "claude-code";
-  version = "1.0.85";
+  version = "1.0.86";
 
   nodejs = nodejs_20; # required for sandboxed Nix builds on Darwin
 
   src = fetchzip {
     url = "https://registry.npmjs.org/@anthropic-ai/claude-code/-/claude-code-${version}.tgz";
-    hash = "sha256-CLqvcolG94JBC5VFlsfybZ9OXe81gJBzKU6Xgr7CGWo=";
+    hash = "sha256-mVXS75KgeKgD7EI5t9X6+TkwjBFyBLOo4/m50sS9XdA=";
   };
 
-  npmDepsHash = "sha256-V0rjoKdXGRNNKRJqPvVIqCQpqgNCklPTVRExCCxbe8g=";
+  npmDepsHash = "sha256-BXpySywlTI19xMaRbJkqBpzbfr8lzAYdpn4dSonmWWg=";
 
   postPatch = ''
     cp ${./package-lock.json} package-lock.json
diff --git a/pkgs/tools/networking/dnstracer/default.nix b/pkgs/by-name/dn/dnstracer/package.nix
similarity index 96%
rename from pkgs/tools/networking/dnstracer/default.nix
rename to pkgs/by-name/dn/dnstracer/package.nix
index e182a086771d..dcff3ee47780 100644
--- a/pkgs/tools/networking/dnstracer/default.nix
+++ b/pkgs/by-name/dn/dnstracer/package.nix
@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  libresolv,
+  darwin,
   perl,
 }:
 
@@ -31,7 +31,7 @@ stdenv.mkDerivation rec {
     install -Dm755 -t $man/share/man/man8 dnstracer.8
   '';
 
-  buildInputs = [ ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ libresolv ];
+  buildInputs = [ ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ darwin.libresolv ];
 
   NIX_LDFLAGS = lib.optionalString stdenv.hostPlatform.isDarwin "-lresolv";
 
diff --git a/pkgs/misc/drivers/epkowa/firmware_location.patch b/pkgs/by-name/ep/epkowa/firmware_location.patch
similarity index 100%
rename from pkgs/misc/drivers/epkowa/firmware_location.patch
rename to pkgs/by-name/ep/epkowa/firmware_location.patch
diff --git a/pkgs/misc/drivers/epkowa/default.nix b/pkgs/by-name/ep/epkowa/package.nix
similarity index 99%
rename from pkgs/misc/drivers/epkowa/default.nix
rename to pkgs/by-name/ep/epkowa/package.nix
index d503490c6120..64fb690f8f86 100644
--- a/pkgs/misc/drivers/epkowa/default.nix
+++ b/pkgs/by-name/ep/epkowa/package.nix
@@ -474,7 +474,7 @@ in
 let
   fwdir = symlinkJoin {
     name = "esci-firmware-dir";
-    paths = lib.mapAttrsToList (name: value: value + /share/esci) plugins;
+    paths = lib.mapAttrsToList (name: value: value + "/share/esci") plugins;
   };
 in
 let
diff --git a/pkgs/misc/drivers/epkowa/sscanf.patch b/pkgs/by-name/ep/epkowa/sscanf.patch
similarity index 100%
rename from pkgs/misc/drivers/epkowa/sscanf.patch
rename to pkgs/by-name/ep/epkowa/sscanf.patch
diff --git a/pkgs/os-specific/linux/kernel/gpio-utils.nix b/pkgs/by-name/gp/gpio-utils/package.nix
similarity index 100%
rename from pkgs/os-specific/linux/kernel/gpio-utils.nix
rename to pkgs/by-name/gp/gpio-utils/package.nix
diff --git a/pkgs/by-name/gr/grpc-gateway/package.nix b/pkgs/by-name/gr/grpc-gateway/package.nix
index 1f9dc8232834..6c6ea6a78097 100644
--- a/pkgs/by-name/gr/grpc-gateway/package.nix
+++ b/pkgs/by-name/gr/grpc-gateway/package.nix
@@ -8,16 +8,16 @@
 
 buildGoModule rec {
   pname = "grpc-gateway";
-  version = "2.27.1";
+  version = "2.27.2";
 
   src = fetchFromGitHub {
     owner = "grpc-ecosystem";
     repo = "grpc-gateway";
     tag = "v${version}";
-    sha256 = "sha256-a7i3tONdSzKq0pWx3okIu65XFTFcXbJd21UItCFz7TA=";
+    sha256 = "sha256-NWMpCPtZZVa53SR8NqSaDpo6fauB3hHb1PeqNs0OO+M=";
   };
 
-  vendorHash = "sha256-Sa2AOwX0McSGQs1Y0evVhdhpjHNNcgyouOtu6H9/AYI=";
+  vendorHash = "sha256-NYiHnarNAndE3QIKPI51plWNNB9kP2DlpYgW43Uw/gw=";
 
   ldflags = [
     "-X=main.version=${version}"
diff --git a/pkgs/by-name/he/heynote/package.nix b/pkgs/by-name/he/heynote/package.nix
index e9567ad03a8e..4662e2647716 100644
--- a/pkgs/by-name/he/heynote/package.nix
+++ b/pkgs/by-name/he/heynote/package.nix
@@ -7,11 +7,11 @@
 }:
 let
   pname = "heynote";
-  version = "2.4.0";
+  version = "2.5.0";
 
   src = fetchurl {
     url = "https://github.com/heyman/heynote/releases/download/v${version}/Heynote_${version}_x86_64.AppImage";
-    sha256 = "sha256-FWd2nKl722aqU1rtOKhCvtHxV0ahaIEQkfRO2NwtaVk=";
+    sha256 = "sha256-01GWQxauMKwqEp3kbegCwn2lpsobtRjO+6I90wiH9wU=";
   };
 
   appimageContents = appimageTools.extractType2 {
diff --git a/pkgs/tools/backup/httrack/default.nix b/pkgs/by-name/ht/httrack/package.nix
similarity index 100%
rename from pkgs/tools/backup/httrack/default.nix
rename to pkgs/by-name/ht/httrack/package.nix
diff --git a/pkgs/by-name/hw/hwloc/package.nix b/pkgs/by-name/hw/hwloc/package.nix
index 4bc0ed5a1bd2..7b0fcc06a2d0 100644
--- a/pkgs/by-name/hw/hwloc/package.nix
+++ b/pkgs/by-name/hw/hwloc/package.nix
@@ -1,7 +1,8 @@
 {
   lib,
   stdenv,
-  fetchurl,
+  fetchFromGitHub,
+  autoreconfHook,
   pkg-config,
   expat,
   ncurses,
@@ -15,13 +16,15 @@
   cudaPackages,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "hwloc";
   version = "2.12.1";
 
-  src = fetchurl {
-    url = "https://www.open-mpi.org/software/hwloc/v${lib.versions.majorMinor version}/downloads/hwloc-${version}.tar.bz2";
-    hash = "sha256-OKkDKLuGJZ+bsv4dxX/YQeER0eY1gBK+8j39ldIdxms=";
+  src = fetchFromGitHub {
+    owner = "open-mpi";
+    repo = "hwloc";
+    tag = "hwloc-${finalAttrs.version}";
+    hash = "sha256-MM0xDysXv4eayi+y2YIP9CMohPe7gfvhltYUxuApRow=";
   };
 
   configureFlags = [
@@ -30,7 +33,11 @@ stdenv.mkDerivation rec {
   ];
 
   # XXX: libX11 is not directly needed, but needed as a propagated dep of Cairo.
-  nativeBuildInputs = [ pkg-config ] ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
+  nativeBuildInputs = [
+    autoreconfHook
+    pkg-config
+  ]
+  ++ lib.optionals enableCuda [ cudaPackages.cuda_nvcc ];
 
   buildInputs = [
     expat
@@ -98,4 +105,4 @@ stdenv.mkDerivation rec {
     ];
     platforms = lib.platforms.all;
   };
-}
+})
diff --git a/pkgs/misc/jackaudio/tools.nix b/pkgs/by-name/ja/jack-example-tools/package.nix
similarity index 94%
rename from pkgs/misc/jackaudio/tools.nix
rename to pkgs/by-name/ja/jack-example-tools/package.nix
index 976cab0e16c8..dc7faf4849fa 100644
--- a/pkgs/misc/jackaudio/tools.nix
+++ b/pkgs/by-name/ja/jack-example-tools/package.nix
@@ -8,7 +8,7 @@
   meson,
   ninja,
 
-  jack,
+  jack2,
   alsa-lib,
   libopus,
   libsamplerate,
@@ -41,8 +41,8 @@ stdenv.mkDerivation (final: {
     ninja
   ];
   buildInputs = [
-    jack
-    libopus
+    jack2
+    (libopus.override { withCustomModes = true; })
     libsamplerate
     libsndfile
     readline
diff --git a/pkgs/misc/jackaudio/jack1.nix b/pkgs/by-name/ja/jack1/package.nix
similarity index 100%
rename from pkgs/misc/jackaudio/jack1.nix
rename to pkgs/by-name/ja/jack1/package.nix
diff --git a/pkgs/misc/jackaudio/default.nix b/pkgs/by-name/ja/jack2/package.nix
similarity index 100%
rename from pkgs/misc/jackaudio/default.nix
rename to pkgs/by-name/ja/jack2/package.nix
diff --git a/pkgs/by-name/jj/jjui/package.nix b/pkgs/by-name/jj/jjui/package.nix
index 23e6da63b086..88b1ee75e373 100644
--- a/pkgs/by-name/jj/jjui/package.nix
+++ b/pkgs/by-name/jj/jjui/package.nix
@@ -7,13 +7,13 @@
 }:
 buildGoModule (finalAttrs: {
   pname = "jjui";
-  version = "0.9.1";
+  version = "0.9.2";
 
   src = fetchFromGitHub {
     owner = "idursun";
     repo = "jjui";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-XWsHkfakSVQZtmN21exUc62is6qT3jw/1FF9RNaW0Uo=";
+    hash = "sha256-8jLQ9KLMMz4y7pXA9wlHbGN4cxRAYVPy6oRKLHCU4SM=";
   };
 
   vendorHash = "sha256-2rlfR5HLFJyLVSRiUGTCwQDFWRBt4jmL6sdZcq7blaE=";
diff --git a/pkgs/by-name/ka/kardolus-chatgpt-cli/package.nix b/pkgs/by-name/ka/kardolus-chatgpt-cli/package.nix
index a2f3995b0976..0444f9c523e4 100644
--- a/pkgs/by-name/ka/kardolus-chatgpt-cli/package.nix
+++ b/pkgs/by-name/ka/kardolus-chatgpt-cli/package.nix
@@ -9,18 +9,18 @@ buildGoModule (finalAttrs: {
   # "chatgpt-cli" is taken by another package with the same upsteam name.
   # To keep "pname" and "package attribute name" identical, the owners name (kardolus) gets prefixed as identifier.
   pname = "kardolus-chatgpt-cli";
-  version = "1.8.7";
+  version = "1.8.8";
 
   src = fetchFromGitHub {
     owner = "kardolus";
     repo = "chatgpt-cli";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-NQoWUF5AcDejkricC7+aP30nGqh/xEwSdb8JWtbd1+w=";
+    hash = "sha256-KdE4TzCkqIzs8xPYflHFpWqpUKqMMxy1YwfNRvyLc08=";
   };
 
   vendorHash = null;
   # The tests of kardolus/chatgpt-cli require an OpenAI API Key to be present in the environment,
-  # (e.g. https://github.com/kardolus/chatgpt-cli/blob/v1.8.7/test/contract/contract_test.go#L35)
+  # (e.g. https://github.com/kardolus/chatgpt-cli/blob/v1.8.8/test/contract/contract_test.go#L35)
   # which will not be the case in the pipeline.
   # Therefore, tests must be skipped.
   doCheck = false;
diff --git a/pkgs/applications/graphics/kodelife/default.nix b/pkgs/by-name/ko/kodelife/package.nix
similarity index 96%
rename from pkgs/applications/graphics/kodelife/default.nix
rename to pkgs/by-name/ko/kodelife/package.nix
index 10acce631f6d..029f64b67365 100644
--- a/pkgs/applications/graphics/kodelife/default.nix
+++ b/pkgs/by-name/ko/kodelife/package.nix
@@ -8,8 +8,7 @@
   alsa-lib,
   curl,
   avahi,
-  gstreamer,
-  gst-plugins-base,
+  gst_all_1,
   libxcb,
   libX11,
   libXcursor,
@@ -78,8 +77,8 @@ stdenv.mkDerivation rec {
   buildInputs = [
     (lib.getLib stdenv.cc.cc)
     alsa-lib
-    gstreamer
-    gst-plugins-base
+    gst_all_1.gstreamer
+    gst_all_1.gst-plugins-base
   ];
 
   installPhase = ''
diff --git a/pkgs/applications/graphics/kodelife/update.sh b/pkgs/by-name/ko/kodelife/update.sh
similarity index 100%
rename from pkgs/applications/graphics/kodelife/update.sh
rename to pkgs/by-name/ko/kodelife/update.sh
diff --git a/pkgs/development/libraries/kompute/default.nix b/pkgs/by-name/ko/kompute/package.nix
similarity index 98%
rename from pkgs/development/libraries/kompute/default.nix
rename to pkgs/by-name/ko/kompute/package.nix
index 61da508306c6..a0598a632626 100644
--- a/pkgs/development/libraries/kompute/default.nix
+++ b/pkgs/by-name/ko/kompute/package.nix
@@ -6,7 +6,7 @@
   cmake,
   vulkan-headers,
   vulkan-loader,
-  fmt,
+  fmt_10,
   spdlog,
   glslang,
   ninja,
@@ -50,7 +50,7 @@ stdenv.mkDerivation rec {
     ninja
   ];
   buildInputs = [
-    fmt
+    fmt_10
     spdlog
   ];
   propagatedBuildInputs = [
diff --git a/pkgs/by-name/ku/kuzu/package.nix b/pkgs/by-name/ku/kuzu/package.nix
index a49c0b73884b..cf49ef4cc6e0 100644
--- a/pkgs/by-name/ku/kuzu/package.nix
+++ b/pkgs/by-name/ku/kuzu/package.nix
@@ -10,13 +10,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "kuzu";
-  version = "0.11.1";
+  version = "0.11.2";
 
   src = fetchFromGitHub {
     owner = "kuzudb";
     repo = "kuzu";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-rRnzAEQhmqO8w+dN0liLGoHympgU5Q/qbsrJqzKpuTw=";
+    hash = "sha256-tRDTDEK//Fy43x6JOTwBlpSwvw50nlY7qdJ30SHbgRM=";
   };
 
   outputs = [
diff --git a/pkgs/by-name/la/lanraragi/package.nix b/pkgs/by-name/la/lanraragi/package.nix
index 41d8dad607b1..fc60ab757c39 100644
--- a/pkgs/by-name/la/lanraragi/package.nix
+++ b/pkgs/by-name/la/lanraragi/package.nix
@@ -30,6 +30,7 @@ buildNpmPackage rec {
 
   nativeBuildInputs = [
     perl
+    perl.pkgs.Appcpanminus
     makeBinaryWrapper
   ];
 
@@ -77,8 +78,7 @@ buildNpmPackage rec {
     runHook preBuild
 
     # Check if every perl dependency was installed
-    # explicitly call cpanm with perl because the shebang is broken on darwin
-    perl ${perl.pkgs.Appcpanminus}/bin/cpanm --installdeps ./tools --notest
+    cpanm --installdeps ./tools --notest
 
     perl ./tools/install.pl install-full
     rm -r node_modules public/js/vendor/*.map public/css/vendor/*.map
diff --git a/pkgs/by-name/li/librewolf-bin-unwrapped/package.nix b/pkgs/by-name/li/librewolf-bin-unwrapped/package.nix
index 1f9c238d409e..acd5fa5bfc48 100644
--- a/pkgs/by-name/li/librewolf-bin-unwrapped/package.nix
+++ b/pkgs/by-name/li/librewolf-bin-unwrapped/package.nix
@@ -37,7 +37,7 @@ let
 
   pname = "librewolf-bin-unwrapped";
 
-  version = "141.0.3-1";
+  version = "142.0-1";
 in
 
 stdenv.mkDerivation {
@@ -47,9 +47,9 @@ stdenv.mkDerivation {
     url = "https://gitlab.com/api/v4/projects/44042130/packages/generic/librewolf/${version}/librewolf-${version}-${arch}-package.tar.xz";
     hash =
       {
-        i686-linux = "sha256-B3fTYNV6kHDo+Ae5r02oXIvcrzlnaZuOO/bAevjU3mk=";
-        x86_64-linux = "sha256-bIKqHQS4daqAQcbXHxLjWdK5MFrSg5ctzfhKe2OrO5c=";
-        aarch64-linux = "sha256-JPidpVXQ8DOwpmBUQn/aBJfydrUSfl6ekgnxCjL7Vgg=";
+        i686-linux = "sha256-2A5pSh2mKKhBiNgAoU4rvNxAm/XjhwZeeyCk6SSetdw=";
+        x86_64-linux = "sha256-dxGDR0Kb+InjCRCKdK6zBhn1qULdK1eQHf7/npPL58w=";
+        aarch64-linux = "sha256-u5eMu+o8Ne3Cvrc+HPv/hFunRpz1F/DOvxZDI65ux0A=";
       }
       .${stdenv.hostPlatform.system} or throwSystem;
   };
diff --git a/pkgs/by-name/mi/miniflux/package.nix b/pkgs/by-name/mi/miniflux/package.nix
index 4a9ea40bd4cf..f9214e1561ee 100644
--- a/pkgs/by-name/mi/miniflux/package.nix
+++ b/pkgs/by-name/mi/miniflux/package.nix
@@ -9,16 +9,16 @@
 
 buildGoModule rec {
   pname = "miniflux";
-  version = "2.2.11";
+  version = "2.2.12";
 
   src = fetchFromGitHub {
     owner = "miniflux";
     repo = "v2";
     tag = version;
-    hash = "sha256-0gheLIwokJWanCOU1gWFyY6KBLqX+02plSp+iLHxd/Y=";
+    hash = "sha256-DeSNI2GFqRF4jdfly44nohCPE4vOXKSaaCkHgKwS4Vs=";
   };
 
-  vendorHash = "sha256-hBvMAPmoGbxz3bV1NCA5nuNC7yv8v8h19pWCispLV3c=";
+  vendorHash = "sha256-bMm2U+4pzafMD2BoRVbwEkzixOgWqw5eGAmw+OCJ9kQ=";
 
   nativeBuildInputs = [ installShellFiles ];
 
diff --git a/pkgs/by-name/mo/models-dev/package.nix b/pkgs/by-name/mo/models-dev/package.nix
index 78151af5cc2b..01ca64b30fcf 100644
--- a/pkgs/by-name/mo/models-dev/package.nix
+++ b/pkgs/by-name/mo/models-dev/package.nix
@@ -9,20 +9,20 @@
 
 let
   models-dev-node-modules-hash = {
-    "aarch64-darwin" = "sha256-VkqxZF2LkNBoIkbQGz98O+y7LgLqQ+FofV2WyMOOUEs=";
-    "aarch64-linux" = "sha256-P7Dik1bXWdipzs4orPff53bDwEXYFHSC05RV789mrTI=";
-    "x86_64-darwin" = "sha256-/VdwzrV+srDrexvXHLKtN2Od24XlXVDWu6pEk1zLtjM=";
-    "x86_64-linux" = "sha256-hMiCOMskK9kwGKaixsvodUVsOuuageiUAwxp/AvzR44=";
+    "aarch64-darwin" = "sha256-IM88XPfttZouN2DEtnWJmbdRxBs8wN7AZ1T28INJlBY=";
+    "aarch64-linux" = "sha256-brjdEEYBJ1R5pIkIHyOOmVieTJ0yUJEgxs7MtbzcKXo=";
+    "x86_64-darwin" = "sha256-aGUWZwySmo0ojOBF/PioZ2wp4NRwYyoaJuytzeGYjck=";
+    "x86_64-linux" = "sha256-Uajwvce9EO1UwmpkGrViOrxlm2R/VnnMK8WAiOiQOhY=";
   };
 in
 stdenvNoCC.mkDerivation (finalAttrs: {
   pname = "models-dev";
-  version = "0-unstable-2025-08-15";
+  version = "0-unstable-2025-08-21";
   src = fetchFromGitHub {
     owner = "sst";
     repo = "models.dev";
-    rev = "f42ddd35b77a47bf11078096871a25a13d46a596";
-    hash = "sha256-OomKQ61KvOMxQ2InwFLIZqoyQ8bMV0S0nx67gREt97g=";
+    rev = "7d417bd1b54bfff3c63f2bc2cc486e6b2700a18d";
+    hash = "sha256-9p+Fc21slH0R7YLJOAlVPS+ZPv+I9j745lGYz6+ln/c=";
   };
 
   node_modules = stdenvNoCC.mkDerivation {
@@ -49,7 +49,8 @@ stdenvNoCC.mkDerivation (finalAttrs: {
        bun install \
          --force \
          --frozen-lockfile \
-         --no-progress
+         --no-progress \
+         --production
 
       runHook postBuild
     '';
diff --git a/pkgs/development/libraries/mongocxx/default.nix b/pkgs/by-name/mo/mongocxx/package.nix
similarity index 100%
rename from pkgs/development/libraries/mongocxx/default.nix
rename to pkgs/by-name/mo/mongocxx/package.nix
diff --git a/pkgs/by-name/ne/netbird/package.nix b/pkgs/by-name/ne/netbird/package.nix
index 30978285cb91..5a2c90693b41 100644
--- a/pkgs/by-name/ne/netbird/package.nix
+++ b/pkgs/by-name/ne/netbird/package.nix
@@ -68,16 +68,16 @@ let
 in
 buildGoModule (finalAttrs: {
   pname = "netbird-${componentName}";
-  version = "0.54.0";
+  version = "0.55.1";
 
   src = fetchFromGitHub {
     owner = "netbirdio";
     repo = "netbird";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-qKYJa7q7scEbbxLHaosaurrjXR5ABxCAnuUcy80yKEc=";
+    hash = "sha256-Bi5vHxKdl9eWWdTB7td+rHuvjt6Ic4kjytWzHJTpCtQ=";
   };
 
-  vendorHash = "sha256-uVVm+iDGP2eZ5GVXWJrWZQ7LpHdZccRIiHPIFs6oAPo=";
+  vendorHash = "sha256-C9qw6VDh+q1UD+Bc+cFAUjIzIXpQAy46cPdyfXwgBSA=";
 
   nativeBuildInputs = [ installShellFiles ] ++ lib.optional (componentName == "ui") pkg-config;
 
diff --git a/pkgs/development/misc/newlib/default.nix b/pkgs/by-name/ne/newlib/package.nix
similarity index 100%
rename from pkgs/development/misc/newlib/default.nix
rename to pkgs/by-name/ne/newlib/package.nix
diff --git a/pkgs/tools/package-management/nix-index/default.nix b/pkgs/by-name/ni/nix-index-unwrapped/package.nix
similarity index 100%
rename from pkgs/tools/package-management/nix-index/default.nix
rename to pkgs/by-name/ni/nix-index-unwrapped/package.nix
diff --git a/pkgs/tools/package-management/nix-index/wrapper.nix b/pkgs/by-name/ni/nix-index/package.nix
similarity index 100%
rename from pkgs/tools/package-management/nix-index/wrapper.nix
rename to pkgs/by-name/ni/nix-index/package.nix
diff --git a/pkgs/tools/package-management/nix-update-source/default.nix b/pkgs/by-name/ni/nix-update-source/package.nix
similarity index 100%
rename from pkgs/tools/package-management/nix-update-source/default.nix
rename to pkgs/by-name/ni/nix-update-source/package.nix
diff --git a/pkgs/data/misc/nixos-artwork/grub2-theme.nix b/pkgs/by-name/ni/nixos-grub2-theme/package.nix
similarity index 100%
rename from pkgs/data/misc/nixos-artwork/grub2-theme.nix
rename to pkgs/by-name/ni/nixos-grub2-theme/package.nix
diff --git a/pkgs/data/misc/nixos-artwork/icons.nix b/pkgs/by-name/ni/nixos-icons/package.nix
similarity index 100%
rename from pkgs/data/misc/nixos-artwork/icons.nix
rename to pkgs/by-name/ni/nixos-icons/package.nix
diff --git a/pkgs/by-name/od/odafileconverter/package.nix b/pkgs/by-name/od/odafileconverter/package.nix
index 78d18506c27f..60ba539566ae 100644
--- a/pkgs/by-name/od/odafileconverter/package.nix
+++ b/pkgs/by-name/od/odafileconverter/package.nix
@@ -22,12 +22,12 @@ stdenv.mkDerivation rec {
   # To obtain the version you will need to run the following command:
   #
   # dpkg-deb -I ${odafileconverter.src} | grep Version
-  version = "25.12.0.0";
+  version = "26.7.0.0";
 
   src = fetchurl {
     # NB: this URL is not stable (i.e. the underlying file and the corresponding version will change over time)
-    url = "https://www.opendesign.com/guestfiles/get?filename=ODAFileConverter_QT6_lnxX64_8.3dll_25.12.deb";
-    hash = "sha256-bc5gFg7101GKqiKAx1w7DpoO24d3JpFccPKUUAfOrdw=";
+    url = "https://www.opendesign.com/guestfiles/get?filename=ODAFileConverter_QT6_lnxX64_8.3dll_26.7.deb";
+    hash = "sha256-MqST9Se66OJ+L0IKzuZkkFjCl3nb07gTO17j+lOWrHI=";
   };
 
   buildInputs = [
diff --git a/pkgs/by-name/op/open-vm-tools/package.nix b/pkgs/by-name/op/open-vm-tools/package.nix
index d038aa0f1ced..8cd5040ace23 100644
--- a/pkgs/by-name/op/open-vm-tools/package.nix
+++ b/pkgs/by-name/op/open-vm-tools/package.nix
@@ -12,6 +12,7 @@
   xercesc,
   icu,
   libdnet,
+  pciutils,
   procps,
   libtirpc,
   rpcsvc-proto,
@@ -107,30 +108,45 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   postPatch = ''
-    sed -i Makefile.am \
-      -e 's,etc/vmware-tools,''${prefix}/etc/vmware-tools,'
-    sed -i scripts/Makefile.am \
-      -e 's,^confdir = ,confdir = ''${prefix},' \
-      -e 's,usr/bin,''${prefix}/usr/bin,'
-    sed -i services/vmtoolsd/Makefile.am \
-      -e 's,etc/vmware-tools,''${prefix}/etc/vmware-tools,' \
-      -e 's,$(PAM_PREFIX),''${prefix}/$(PAM_PREFIX),'
-    sed -i vgauth/service/Makefile.am \
-      -e 's,/etc/vmware-tools/vgauth/schemas,''${prefix}/etc/vmware-tools/vgauth/schemas,' \
-      -e 's,$(DESTDIR)/etc/vmware-tools/vgauth.conf,''${prefix}/etc/vmware-tools/vgauth.conf,'
+    substituteInPlace Makefile.am \
+      --replace-fail "etc/vmware-tools" "''${prefix}/etc/vmware-tools"
+    substituteInPlace scripts/Makefile.am \
+      --replace-fail "confdir = /etc/vmware-tools" "confdir = ''${prefix}/etc/vmware-tools" \
+      --replace-fail "/usr/bin" "''${prefix}/bin"
+    substituteInPlace services/vmtoolsd/Makefile.am \
+      --replace-fail "etc/vmware-tools" "''${prefix}/etc/vmware-tools" \
+      --replace-fail "\$(PAM_PREFIX)" "''${prefix}/\$(PAM_PREFIX)"
+    substituteInPlace vgauth/service/Makefile.am \
+      --replace-fail "/etc/vmware-tools/vgauth/schemas" "''${prefix}/etc/vmware-tools/vgauth/schemas" \
+      --replace-fail "\$(DESTDIR)/etc/vmware-tools/vgauth.conf" "''${prefix}/etc/vmware-tools/vgauth.conf"
 
     # don't abort on any warning
-    sed -i 's,CFLAGS="$CFLAGS -Werror",,' configure.ac
+    substituteInPlace configure.ac \
+      --replace-fail 'CFLAGS="$CFLAGS -Werror"' ""
 
     # Make reboot work, shutdown is not in /sbin on NixOS
-    sed -i 's,/sbin/shutdown,shutdown,' lib/system/systemLinux.c
+    substituteInPlace lib/system/systemLinux.c \
+      --replace-fail "/sbin/shutdown" "shutdown"
 
     # Fix paths to fuse3 (we do not use fuse2 so that is not modified)
-    sed -i 's,/bin/fusermount3,${fuse3}/bin/fusermount3,' vmhgfs-fuse/config.c
+    substituteInPlace vmhgfs-fuse/config.c \
+      --replace-fail "/bin/fusermount3" "${fuse3}/bin/fusermount3"
+
+    # do not break the PATHs set by makeWrapper, sudo resets PATH anyway.
+    substituteInPlace scripts/common/vm-support \
+      --replace-fail "export PATH=/bin:/sbin:/usr/bin:/usr/sbin" "" \
+      --replace-fail ". /etc/profile" ":" \
+      --replace-fail "/sbin/lsmod" "lsmod"
 
     substituteInPlace services/plugins/vix/foundryToolsDaemon.c \
      --replace-fail "/usr/bin/vmhgfs-fuse" "${placeholder "out"}/bin/vmhgfs-fuse" \
      --replace-fail "/bin/mount" "${util-linux}/bin/mount"
+
+    substituteInPlace lib/guestStoreClientHelper/guestStoreClient.c \
+      --replace-fail "libguestStoreClient.so.0" "$out/lib/libguestStoreClient.so.0"
+
+    substituteInPlace udev/99-vmware-scsi-udev.rules \
+      --replace-fail "/bin/sh" "${bash}/bin/sh"
   '';
 
   configureFlags = [
@@ -149,6 +165,16 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   postInstall = ''
+    wrapProgram "$out/bin/vm-support" \
+      --prefix PATH ':' "${
+        makeBinPath [
+          iproute2
+          pciutils # for lspci
+          systemd
+          which
+        ]
+      }"
+
     wrapProgram "$out/etc/vmware-tools/scripts/vmware/network" \
       --prefix PATH ':' "${
         makeBinPath [
@@ -158,7 +184,6 @@ stdenv.mkDerivation (finalAttrs: {
           which
         ]
       }"
-    substituteInPlace "$out/lib/udev/rules.d/99-vmware-scsi-udev.rules" --replace-fail "/bin/sh" "${bash}/bin/sh"
   '';
 
   meta = {
diff --git a/pkgs/by-name/op/opencode/package.nix b/pkgs/by-name/op/opencode/package.nix
index f0f00fdacb39..ec4250eab843 100644
--- a/pkgs/by-name/op/opencode/package.nix
+++ b/pkgs/by-name/op/opencode/package.nix
@@ -13,12 +13,6 @@
 }:
 
 let
-  opencode-node-modules-hash = {
-    "aarch64-darwin" = "sha256-hznCg/7c9uNV7NXTkb6wtn3EhJDkGI7yZmSIA2SqX7g=";
-    "aarch64-linux" = "sha256-hznCg/7c9uNV7NXTkb6wtn3EhJDkGI7yZmSIA2SqX7g=";
-    "x86_64-darwin" = "sha256-hznCg/7c9uNV7NXTkb6wtn3EhJDkGI7yZmSIA2SqX7g=";
-    "x86_64-linux" = "sha256-hznCg/7c9uNV7NXTkb6wtn3EhJDkGI7yZmSIA2SqX7g=";
-  };
   bun-target = {
     "aarch64-darwin" = "bun-darwin-arm64";
     "aarch64-linux" = "bun-linux-arm64";
@@ -28,12 +22,12 @@ let
 in
 stdenvNoCC.mkDerivation (finalAttrs: {
   pname = "opencode";
-  version = "0.5.6";
+  version = "0.5.13";
   src = fetchFromGitHub {
     owner = "sst";
     repo = "opencode";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-dzhthgkAPjvPOxWBnf67OkTwbZ3Htdl68+UDlz45xwI=";
+    hash = "sha256-CzVzBvuK/RRYxFA4wOhkIXuXjoxWHHRnzUpGuvl9kQU=";
   };
 
   tui = buildGoModule {
@@ -107,7 +101,7 @@ stdenvNoCC.mkDerivation (finalAttrs: {
     # Required else we get errors that our fixed-output derivation references store paths
     dontFixup = true;
 
-    outputHash = opencode-node-modules-hash.${stdenvNoCC.hostPlatform.system};
+    outputHash = "sha256-hznCg/7c9uNV7NXTkb6wtn3EhJDkGI7yZmSIA2SqX7g=";
     outputHashAlgo = "sha256";
     outputHashMode = "recursive";
   };
diff --git a/pkgs/tools/admin/pgadmin/check-system-config-dir.patch b/pkgs/by-name/pg/pgadmin4/check-system-config-dir.patch
similarity index 100%
rename from pkgs/tools/admin/pgadmin/check-system-config-dir.patch
rename to pkgs/by-name/pg/pgadmin4/check-system-config-dir.patch
diff --git a/pkgs/tools/admin/pgadmin/expose-setup.py.patch b/pkgs/by-name/pg/pgadmin4/expose-setup.py.patch
similarity index 100%
rename from pkgs/tools/admin/pgadmin/expose-setup.py.patch
rename to pkgs/by-name/pg/pgadmin4/expose-setup.py.patch
diff --git a/pkgs/tools/admin/pgadmin/missing-hashes.json b/pkgs/by-name/pg/pgadmin4/missing-hashes.json
similarity index 100%
rename from pkgs/tools/admin/pgadmin/missing-hashes.json
rename to pkgs/by-name/pg/pgadmin4/missing-hashes.json
diff --git a/pkgs/tools/admin/pgadmin/default.nix b/pkgs/by-name/pg/pgadmin4/package.nix
similarity index 100%
rename from pkgs/tools/admin/pgadmin/default.nix
rename to pkgs/by-name/pg/pgadmin4/package.nix
diff --git a/pkgs/tools/admin/pgadmin/update.sh b/pkgs/by-name/pg/pgadmin4/update.sh
similarity index 94%
rename from pkgs/tools/admin/pgadmin/update.sh
rename to pkgs/by-name/pg/pgadmin4/update.sh
index 734853b4af1a..de6bfcf81988 100755
--- a/pkgs/tools/admin/pgadmin/update.sh
+++ b/pkgs/by-name/pg/pgadmin4/update.sh
@@ -52,12 +52,12 @@ fi
 printf "Done\n"
 
 if [[ -f missing-hashes.json ]]; then
-  if [[ ! -f "$nixpkgs/pkgs/tools/admin/pgadmin/missing-hashes.json" ]]; then
+  if [[ ! -f "$nixpkgs/pkgs/by-name/pg/pgadmin4/missing-hashes.json" ]]; then
     printf "PLEASE NOTE: FIRST TIME OF FINDING MISSING HASHES!"
     printf "Please add \"missingHashes = ./missing-hashes.json\" to pgadmin derivation"
   fi
   printf "Copy files to nixpkgs\n"
-  cp missing-hashes.json "$nixpkgs/pkgs/tools/admin/pgadmin/"
+  cp missing-hashes.json "$nixpkgs/pkgs/by-name/pg/pgadmin4"
 fi
 
 printf "Done\n"
diff --git a/pkgs/by-name/po/podlet/package.nix b/pkgs/by-name/po/podlet/package.nix
index 5369aaf28c3d..c55a43ae0f60 100644
--- a/pkgs/by-name/po/podlet/package.nix
+++ b/pkgs/by-name/po/podlet/package.nix
@@ -22,7 +22,7 @@ rustPlatform.buildRustPackage rec {
     homepage = "https://github.com/containers/podlet";
     changelog = "https://github.com/containers/podlet/blob/v${version}/CHANGELOG.md";
     license = lib.licenses.mpl20;
-    maintainers = with lib.maintainers; [ qwqawawow ];
+    maintainers = with lib.maintainers; [ eihqnh ];
     mainProgram = "podlet";
   };
 }
diff --git a/pkgs/by-name/re/recastnavigation/package.nix b/pkgs/by-name/re/recastnavigation/package.nix
index b93d17aecbb9..716c577b8b44 100644
--- a/pkgs/by-name/re/recastnavigation/package.nix
+++ b/pkgs/by-name/re/recastnavigation/package.nix
@@ -6,31 +6,23 @@
   libGL,
   SDL2,
   libGLU,
-  catch,
+  catch2_3,
 }:
 
 stdenv.mkDerivation {
   pname = "recastai";
-  # use latest revision for the CMake build process and OpenMW
+  # use latest revision for CMake v4
   # OpenMW use e75adf86f91eb3082220085e42dda62679f9a3ea
-  version = "unstable-2023-01-02";
+  version = "unstable-2025-08-12";
 
   src = fetchFromGitHub {
     owner = "recastnavigation";
     repo = "recastnavigation";
-    rev = "405cc095ab3a2df976a298421974a2af83843baf";
-    sha256 = "sha256-WVzDI7+UuAl10Tm1Zjkea/FMk0cIe7pWg0iyFLbwAdI=";
+    rev = "40ec6fcd6c0263a3d7798452aee531066072d15d";
+    hash = "sha256-4flJMJsuCecpHDtgAsnDU7WoAtUg/XJfRXx096Zw6bE=";
   };
 
-  postPatch = ''
-    cp ${catch}/include/catch/catch.hpp Tests/catch.hpp
-
-    # https://github.com/recastnavigation/recastnavigation/issues/524
-    substituteInPlace CMakeLists.txt \
-      --replace '\$'{exec_prefix}/'$'{CMAKE_INSTALL_LIBDIR} '$'{CMAKE_INSTALL_FULL_LIBDIR} \
-      --replace '\$'{prefix}/'$'{CMAKE_INSTALL_INCLUDEDIR} '$'{CMAKE_INSTALL_FULL_INCLUDEDIR}
-  ''
-  + lib.optionalString stdenv.hostPlatform.isDarwin ''
+  postPatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
     # Expects SDL2.framework in specific location, which we don't have
     # Change where SDL2 headers are searched for to match what we do have
     substituteInPlace RecastDemo/CMakeLists.txt \
@@ -40,6 +32,7 @@ stdenv.mkDerivation {
   doCheck = true;
 
   nativeBuildInputs = [ cmake ];
+  checkInputs = [ catch2_3 ];
 
   buildInputs = [
     libGL
@@ -47,12 +40,12 @@ stdenv.mkDerivation {
     libGLU
   ];
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/recastnavigation/recastnavigation";
     description = "Navigation-mesh Toolset for Games";
     mainProgram = "RecastDemo";
-    license = licenses.zlib;
-    maintainers = with maintainers; [ marius851000 ];
-    platforms = platforms.all;
+    license = lib.licenses.zlib;
+    maintainers = with lib.maintainers; [ marius851000 ];
+    platforms = lib.platforms.all;
   };
 }
diff --git a/pkgs/by-name/re/rerun/package.nix b/pkgs/by-name/re/rerun/package.nix
index d5ffb129de56..acf6d0799335 100644
--- a/pkgs/by-name/re/rerun/package.nix
+++ b/pkgs/by-name/re/rerun/package.nix
@@ -107,10 +107,11 @@ rustPlatform.buildRustPackage (finalAttrs: {
   env =
     let
       inherit (llvmPackages) clang-unwrapped;
-      major-version = builtins.head (builtins.splitVersion clang-unwrapped.version);
+      majorVersion = lib.versions.major clang-unwrapped.version;
+
       # resource dir + builtins from the unwrapped clang
-      resourceDir = "${lib.getLib clang-unwrapped}/lib/clang/${major-version}";
-      includeDir = "${lib.getLib llvmPackages.libclang}/lib/clang/${major-version}/include";
+      resourceDir = "${lib.getLib clang-unwrapped}/lib/clang/${majorVersion}";
+      includeDir = "${lib.getLib llvmPackages.libclang}/lib/clang/${majorVersion}/include";
     in
     {
       CC_wasm32_unknown_unknown = lib.getExe clang-unwrapped;
diff --git a/pkgs/tools/filesystems/romdirfs/default.nix b/pkgs/by-name/ro/romdirfs/package.nix
similarity index 93%
rename from pkgs/tools/filesystems/romdirfs/default.nix
rename to pkgs/by-name/ro/romdirfs/package.nix
index 387d17ce1861..00b6543cc1ac 100644
--- a/pkgs/tools/filesystems/romdirfs/default.nix
+++ b/pkgs/by-name/ro/romdirfs/package.nix
@@ -1,13 +1,13 @@
 {
   lib,
-  stdenv,
+  gccStdenv,
   fetchFromGitHub,
   cmake,
   pkg-config,
   fuse,
 }:
 
-stdenv.mkDerivation rec {
+gccStdenv.mkDerivation rec {
   pname = "romdirfs";
   version = "1.2";
 
diff --git a/pkgs/by-name/so/source-meta-json-schema/package.nix b/pkgs/by-name/so/source-meta-json-schema/package.nix
index c2e2216aadda..c8fb16197637 100644
--- a/pkgs/by-name/so/source-meta-json-schema/package.nix
+++ b/pkgs/by-name/so/source-meta-json-schema/package.nix
@@ -5,7 +5,7 @@
   cmake,
 }:
 let
-  version = "10.0.0";
+  version = "11.1.1";
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "source-meta-json-schema";
@@ -15,7 +15,7 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "sourcemeta";
     repo = "jsonschema";
     rev = "v${version}";
-    hash = "sha256-fYNbHU9DcSzMrMt+pDbbtPirTc+Wu4jq+vSqq+qzhtE=";
+    hash = "sha256-eXUiRpZko5ZHf2NVQu9HD+FgR3BxcTB9feNeI0kml+4=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/ta/tailscale/package.nix b/pkgs/by-name/ta/tailscale/package.nix
index 91772517b429..e3533687a464 100644
--- a/pkgs/by-name/ta/tailscale/package.nix
+++ b/pkgs/by-name/ta/tailscale/package.nix
@@ -22,12 +22,9 @@
   tailscale-nginx-auth,
 }:
 
-let
-  version = "1.86.4";
-in
-buildGoModule {
+buildGoModule (finalAttrs: {
   pname = "tailscale";
-  inherit version;
+  version = "1.86.4";
 
   outputs = [
     "out"
@@ -37,7 +34,7 @@ buildGoModule {
   src = fetchFromGitHub {
     owner = "tailscale";
     repo = "tailscale";
-    tag = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-cYj04DtoYKejygz1Euir/6/Eq1M046nzzhqSfpTi0OE=";
   };
 
@@ -70,8 +67,8 @@ buildGoModule {
   ldflags = [
     "-w"
     "-s"
-    "-X tailscale.com/version.longStamp=${version}"
-    "-X tailscale.com/version.shortStamp=${version}"
+    "-X tailscale.com/version.longStamp=${finalAttrs.version}"
+    "-X tailscale.com/version.shortStamp=${finalAttrs.version}"
   ];
 
   tags = [
@@ -223,15 +220,16 @@ buildGoModule {
   meta = {
     homepage = "https://tailscale.com";
     description = "Node agent for Tailscale, a mesh VPN built on WireGuard";
-    changelog = "https://github.com/tailscale/tailscale/releases/tag/v${version}";
+    changelog = "https://tailscale.com/changelog#client";
     license = lib.licenses.bsd3;
     mainProgram = "tailscale";
     maintainers = with lib.maintainers; [
       mbaillie
       jk
       mfrw
+      philiptaron
       pyrox0
       ryan4yin
     ];
   };
-}
+})
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/Gemfile b/pkgs/by-name/te/terraform-landscape/Gemfile
similarity index 100%
rename from pkgs/applications/networking/cluster/terraform-landscape/Gemfile
rename to pkgs/by-name/te/terraform-landscape/Gemfile
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock b/pkgs/by-name/te/terraform-landscape/Gemfile.lock
similarity index 100%
rename from pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock
rename to pkgs/by-name/te/terraform-landscape/Gemfile.lock
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/gemset.nix b/pkgs/by-name/te/terraform-landscape/gemset.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/terraform-landscape/gemset.nix
rename to pkgs/by-name/te/terraform-landscape/gemset.nix
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/default.nix b/pkgs/by-name/te/terraform-landscape/package.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/terraform-landscape/default.nix
rename to pkgs/by-name/te/terraform-landscape/package.nix
diff --git a/pkgs/applications/networking/cluster/terraforming/Gemfile b/pkgs/by-name/te/terraforming/Gemfile
similarity index 100%
rename from pkgs/applications/networking/cluster/terraforming/Gemfile
rename to pkgs/by-name/te/terraforming/Gemfile
diff --git a/pkgs/applications/networking/cluster/terraforming/Gemfile.lock b/pkgs/by-name/te/terraforming/Gemfile.lock
similarity index 100%
rename from pkgs/applications/networking/cluster/terraforming/Gemfile.lock
rename to pkgs/by-name/te/terraforming/Gemfile.lock
diff --git a/pkgs/applications/networking/cluster/terraforming/gemset.nix b/pkgs/by-name/te/terraforming/gemset.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/terraforming/gemset.nix
rename to pkgs/by-name/te/terraforming/gemset.nix
diff --git a/pkgs/applications/networking/cluster/terraforming/default.nix b/pkgs/by-name/te/terraforming/package.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/terraforming/default.nix
rename to pkgs/by-name/te/terraforming/package.nix
diff --git a/pkgs/applications/networking/cluster/tubekit/default.nix b/pkgs/by-name/tu/tubekit-unwrapped/package.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/tubekit/default.nix
rename to pkgs/by-name/tu/tubekit-unwrapped/package.nix
diff --git a/pkgs/applications/networking/cluster/tubekit/wrapper.nix b/pkgs/by-name/tu/tubekit/package.nix
similarity index 100%
rename from pkgs/applications/networking/cluster/tubekit/wrapper.nix
rename to pkgs/by-name/tu/tubekit/package.nix
diff --git a/pkgs/misc/drivers/utsushi/networkscan.nix b/pkgs/by-name/ut/utsushi-networkscan/package.nix
similarity index 100%
rename from pkgs/misc/drivers/utsushi/networkscan.nix
rename to pkgs/by-name/ut/utsushi-networkscan/package.nix
diff --git a/pkgs/misc/drivers/utsushi/default.nix b/pkgs/by-name/ut/utsushi/package.nix
similarity index 100%
rename from pkgs/misc/drivers/utsushi/default.nix
rename to pkgs/by-name/ut/utsushi/package.nix
diff --git a/pkgs/by-name/uu/uutils-diffutils/package.nix b/pkgs/by-name/uu/uutils-diffutils/package.nix
index 7ec5565d7ad9..f5dbfa5d0270 100644
--- a/pkgs/by-name/uu/uutils-diffutils/package.nix
+++ b/pkgs/by-name/uu/uutils-diffutils/package.nix
@@ -35,7 +35,7 @@ rustPlatform.buildRustPackage (finalAttrs: {
     homepage = "https://github.com/uutils/diffutils";
     license = lib.licenses.mit;
     mainProgram = "diffutils";
-    maintainers = with lib.maintainers; [ ];
+    maintainers = with lib.maintainers; [ defelo ];
     platforms = lib.platforms.unix;
   };
 })
diff --git a/pkgs/by-name/vr/vrcx/deps.json b/pkgs/by-name/vr/vrcx/deps.json
index 50b31b992525..38b526ba576f 100644
--- a/pkgs/by-name/vr/vrcx/deps.json
+++ b/pkgs/by-name/vr/vrcx/deps.json
@@ -1,8 +1,8 @@
 [
   {
     "pname": "DiscordRichPresence",
-    "version": "1.3.0.28",
-    "hash": "sha256-KdwSl5ysunAbC21cXRrSROO2XN/ZscIVdq6+IH+5Fbs="
+    "version": "1.5.0.51",
+    "hash": "sha256-ZfyXXsJ7c8u0EAfKjquv/pAL3ZajKLnVIJWADQYJ6wI="
   },
   {
     "pname": "EntityFramework",
@@ -51,13 +51,13 @@
   },
   {
     "pname": "Microsoft.JavaScript.NodeApi",
-    "version": "0.9.11",
-    "hash": "sha256-1F2lG7ePVKy9QXMt76AWf64zj5o9upVik3//AqPaw7U="
+    "version": "0.9.13",
+    "hash": "sha256-zXNmEg6txPXXD3yLHMWlziPgbDsNCLQcmqxO0pU8OCY="
   },
   {
     "pname": "Microsoft.JavaScript.NodeApi.Generator",
-    "version": "0.9.11",
-    "hash": "sha256-WAunMB3ksE0trHmohr+fTxGXiYNd553PUJoDaOSmLxo="
+    "version": "0.9.13",
+    "hash": "sha256-tgWN7EHgXwHvV5f1xXOvaXBVjeM+LfRyhPv7N9625N0="
   },
   {
     "pname": "Microsoft.NETCore.Platforms",
@@ -69,11 +69,6 @@
     "version": "1.1.1",
     "hash": "sha256-8hLiUKvy/YirCWlFwzdejD2Db3DaXhHxT7GSZx/znJg="
   },
-  {
-    "pname": "Microsoft.NETCore.Platforms",
-    "version": "2.0.0",
-    "hash": "sha256-IEvBk6wUXSdyCnkj6tHahOJv290tVVT8tyemYcR0Yro="
-  },
   {
     "pname": "Microsoft.NETCore.Platforms",
     "version": "2.1.2",
@@ -104,11 +99,6 @@
     "version": "4.3.0",
     "hash": "sha256-mBNDmPXNTW54XLnPAUwBRvkIORFM7/j0D0I2SyQPDEg="
   },
-  {
-    "pname": "Microsoft.Win32.Registry",
-    "version": "4.5.0",
-    "hash": "sha256-WMBXsIb0DgPFPaFkNVxY9b9vcMxPqtgFgijKYMJfV/0="
-  },
   {
     "pname": "Microsoft.Win32.Registry",
     "version": "4.7.0",
@@ -116,8 +106,8 @@
   },
   {
     "pname": "Microsoft.Win32.SystemEvents",
-    "version": "9.0.6",
-    "hash": "sha256-iIS1YZ8X8Zfahg2jOW3ODCZwmSSsp96epu+kT+wieQg="
+    "version": "9.0.7",
+    "hash": "sha256-7o59Y4Wy9EsTlcNVCNuweR/7Y7QlbB6MwK/aHGax3F4="
   },
   {
     "pname": "NETStandard.Library",
@@ -136,8 +126,8 @@
   },
   {
     "pname": "NLog",
-    "version": "5.5.0",
-    "hash": "sha256-WkuKGo3iEqJruQuRZXMksqIbAQjZbFIANcm0zZr/fYE="
+    "version": "6.0.2",
+    "hash": "sha256-sToQRwukDjUo3ytSmHXT5p4j6fTv1utHkQKeF48EWnQ="
   },
   {
     "pname": "runtime.any.System.Collections",
@@ -431,18 +421,13 @@
   },
   {
     "pname": "SixLabors.ImageSharp",
-    "version": "3.1.10",
-    "hash": "sha256-6bVTSCxLY8Dt+9lpo4F4xEtMv5oPve2vS76O/lcuIok="
-  },
-  {
-    "pname": "SixLabors.ImageSharp",
-    "version": "3.1.8",
-    "hash": "sha256-cE9BQfbCvJ0Mf+fQiTD8elOZEPcfZHjDz2BHdiO+D08="
+    "version": "3.1.11",
+    "hash": "sha256-MlRF+3SGfahbsB1pZGKMOrsfUCx//hCo7ECrXr03DpA="
   },
   {
     "pname": "SixLabors.ImageSharp.Drawing",
-    "version": "2.1.6",
-    "hash": "sha256-2VYoBw8XidjqFUS03EgxOq9vw/WRZjhF3z1pwfaSzUc="
+    "version": "2.1.7",
+    "hash": "sha256-LkStbMTvIPIXvkda4Xn1simHaH0mJHHuCI0+AaAS4/4="
   },
   {
     "pname": "sqlite-net-pcl",
@@ -491,8 +476,8 @@
   },
   {
     "pname": "System.CodeDom",
-    "version": "9.0.6",
-    "hash": "sha256-vcKv5qTborX8E4Uy7T/hqWRii35Icw1siDWPJenk9K8="
+    "version": "9.0.7",
+    "hash": "sha256-L54rUZDfqPwXDhA0C1t0wtxcFhFrDYowjjyn67+kvLM="
   },
   {
     "pname": "System.Collections",
@@ -576,8 +561,8 @@
   },
   {
     "pname": "System.Drawing.Common",
-    "version": "9.0.6",
-    "hash": "sha256-uQDdDVOu3G39PPa1SbE7bHfTzQBAGzL705UklWl/y2I="
+    "version": "9.0.7",
+    "hash": "sha256-GRiTUzguCr8o3V9whhoKvW16NCA08mdYO1rViJiDvvo="
   },
   {
     "pname": "System.Globalization",
@@ -631,8 +616,8 @@
   },
   {
     "pname": "System.Management",
-    "version": "9.0.6",
-    "hash": "sha256-dZ46TTekJCMfgfRsz6qjJpa0IzPxlm8XXyYmP6msNZY="
+    "version": "9.0.7",
+    "hash": "sha256-CRa1zZHzw1kq8tpFnncV45prHCfYRg8lTYdv0E+E+qw="
   },
   {
     "pname": "System.Memory",
@@ -789,11 +774,6 @@
     "version": "4.3.0",
     "hash": "sha256-P5jHCgMbgFMYiONvzmaKFeOqcAIDPu/U8bOVrNPYKqc="
   },
-  {
-    "pname": "System.Security.AccessControl",
-    "version": "4.5.0",
-    "hash": "sha256-AFsKPb/nTk2/mqH/PYpaoI8PLsiKKimaXf+7Mb5VfPM="
-  },
   {
     "pname": "System.Security.AccessControl",
     "version": "4.7.0",
@@ -859,11 +839,6 @@
     "version": "4.3.0",
     "hash": "sha256-mbdLVUcEwe78p3ZnB6jYsizNEqxMaCAWI3tEQNhRQAE="
   },
-  {
-    "pname": "System.Security.Principal.Windows",
-    "version": "4.5.0",
-    "hash": "sha256-BkUYNguz0e4NJp1kkW7aJBn3dyH9STwB5N8XqnlCsmY="
-  },
   {
     "pname": "System.Security.Principal.Windows",
     "version": "4.7.0",
@@ -886,8 +861,8 @@
   },
   {
     "pname": "System.Text.Json",
-    "version": "9.0.6",
-    "hash": "sha256-WC/QbZhTaoZ3PbDKcFvJwMIA4xLUdnMrAXGlOW87VNY="
+    "version": "9.0.7",
+    "hash": "sha256-f3leKX3r7JoUbKo6tnuIsPVYJHNbElHWffhyqk1+2C0="
   },
   {
     "pname": "System.Text.RegularExpressions",
diff --git a/pkgs/by-name/vr/vrcx/package.nix b/pkgs/by-name/vr/vrcx/package.nix
index a74442d1fd93..c968e75579e6 100644
--- a/pkgs/by-name/vr/vrcx/package.nix
+++ b/pkgs/by-name/vr/vrcx/package.nix
@@ -4,7 +4,7 @@
   buildDotnetModule,
   dotnetCorePackages,
   buildNpmPackage,
-  electron_36,
+  electron_37,
   makeWrapper,
   copyDesktopItems,
   makeDesktopItem,
@@ -12,16 +12,16 @@
 }:
 let
   pname = "vrcx";
-  version = "2025.06.30";
+  version = "2025.08.17";
   dotnet = dotnetCorePackages.dotnet_9;
-  electron = electron_36;
+  electron = electron_37;
 
   src = fetchFromGitHub {
     owner = "vrcx-team";
     repo = "VRCX";
-    # v2025.06.30 tag didn't bump the version
-    rev = "4a630079d778069293a39e5b7f7fdb3f543590da";
-    hash = "sha256-GBSkwfi9uvmBg3crnE9CYKDWzekrPjhSq9kDJzmf3bM=";
+    # v2025.08.17 tag didn't bump the version
+    rev = "fa10af8acaef6ca23866cee6fc80b1b0b0038ca5";
+    hash = "sha256-j/NGym4tGcazDcWtiPqxHbBCbHCkkuysd+cMUPAj6Rc=";
   };
 
   backend = buildDotnetModule {
@@ -46,7 +46,7 @@ in
 buildNpmPackage {
   inherit pname version src;
 
-  npmDepsHash = "sha256-x84l1+gRH2qADofYwyrEOeE4WJwqTqVB0L3JRxbscmM=";
+  npmDepsHash = "sha256-aFbdQhH8lQ/R+o4lCoqVc2nPJnxmNEFjR4MnqWKP32g=";
   npmFlags = [ "--ignore-scripts" ];
   makeCacheWritable = true;
 
@@ -58,6 +58,8 @@ buildNpmPackage {
   buildPhase = ''
     runHook preBuild
 
+    # need to run vue-demi postinstall for pinia
+    node ./node_modules/vue-demi/scripts/postinstall.js
     env PLATFORM=linux npm exec webpack -- --config webpack.config.js --mode production
     node src-electron/patch-package-version.js
     npm exec electron-builder -- --dir \
diff --git a/pkgs/development/interpreters/wasmer/default.nix b/pkgs/by-name/wa/wasmer/package.nix
similarity index 96%
rename from pkgs/development/interpreters/wasmer/default.nix
rename to pkgs/by-name/wa/wasmer/package.nix
index 7415fa2e2003..da8a9fe6ce71 100644
--- a/pkgs/development/interpreters/wasmer/default.nix
+++ b/pkgs/by-name/wa/wasmer/package.nix
@@ -2,7 +2,7 @@
   lib,
   rustPlatform,
   fetchFromGitHub,
-  llvmPackages,
+  llvmPackages_18,
   libffi,
   libxml2,
   withLLVM ? true,
@@ -27,7 +27,7 @@ rustPlatform.buildRustPackage rec {
   ];
 
   buildInputs = lib.optionals withLLVM [
-    llvmPackages.llvm
+    llvmPackages_18.llvm
     libffi
     libxml2
   ];
@@ -50,7 +50,7 @@ rustPlatform.buildRustPackage rec {
     "wasmer"
   ];
 
-  env.LLVM_SYS_180_PREFIX = lib.optionalString withLLVM llvmPackages.llvm.dev;
+  env.LLVM_SYS_180_PREFIX = lib.optionalString withLLVM llvmPackages_18.llvm.dev;
 
   # Tests are failing due to `Cannot allocate memory` and other reasons
   doCheck = false;
diff --git a/pkgs/development/interpreters/wavm/default.nix b/pkgs/by-name/wa/wavm/package.nix
similarity index 85%
rename from pkgs/development/interpreters/wavm/default.nix
rename to pkgs/by-name/wa/wavm/package.nix
index 82ee3fee4eb6..d56fba46cb56 100644
--- a/pkgs/development/interpreters/wavm/default.nix
+++ b/pkgs/by-name/wa/wavm/package.nix
@@ -1,11 +1,11 @@
 {
   lib,
-  llvmPackages,
+  llvmPackages_12,
   fetchFromGitHub,
   cmake,
 }:
 
-llvmPackages.stdenv.mkDerivation (finalAttrs: {
+llvmPackages_12.stdenv.mkDerivation (finalAttrs: {
   pname = "wavm";
   version = "2022-05-14";
 
@@ -18,7 +18,7 @@ llvmPackages.stdenv.mkDerivation (finalAttrs: {
 
   nativeBuildInputs = [
     cmake
-    llvmPackages.llvm
+    llvmPackages_12.llvm
   ];
 
   meta = with lib; {
diff --git a/pkgs/by-name/wa/waydroid-helper/package.nix b/pkgs/by-name/wa/waydroid-helper/package.nix
index 81fa878b05ab..5380a61c29d1 100644
--- a/pkgs/by-name/wa/waydroid-helper/package.nix
+++ b/pkgs/by-name/wa/waydroid-helper/package.nix
@@ -14,6 +14,7 @@
   bash,
   bindfs,
   dbus,
+  android-tools,
   e2fsprogs,
   fakeroot,
   fuse,
@@ -83,6 +84,7 @@ python3Packages.buildPythonApplication {
     httpx
     pygobject3
     pyyaml
+    pywayland
   ];
 
   strictDeps = true;
@@ -93,6 +95,7 @@ python3Packages.buildPythonApplication {
     "\${gappsWrapperArgs[@]}"
     "--prefix PATH : ${
       lib.makeBinPath [
+        android-tools
         bindfs
         e2fsprogs
         fakeroot
diff --git a/pkgs/development/libraries/webkit2-sharp/default.nix b/pkgs/by-name/we/webkit2-sharp/package.nix
similarity index 95%
rename from pkgs/development/libraries/webkit2-sharp/default.nix
rename to pkgs/by-name/we/webkit2-sharp/package.nix
index 78b89397b76d..e50da66aa854 100644
--- a/pkgs/development/libraries/webkit2-sharp/default.nix
+++ b/pkgs/by-name/we/webkit2-sharp/package.nix
@@ -7,7 +7,7 @@
   libxslt,
   mono,
   pkg-config,
-  webkitgtk,
+  webkitgtk_4_0,
 }:
 
 stdenv.mkDerivation rec {
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     gtk-sharp-3_0
-    webkitgtk
+    webkitgtk_4_0
   ];
 
   postPatch = ''
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
   installFlags = [ "GAPIXMLDIR=/tmp/gapixml" ];
 
   passthru = {
-    inherit webkitgtk;
+    webkitgtk = webkitgtk_4_0;
   };
 
   meta = {
diff --git a/pkgs/applications/misc/wikicurses/default.nix b/pkgs/by-name/wi/wikicurses/package.nix
similarity index 88%
rename from pkgs/applications/misc/wikicurses/default.nix
rename to pkgs/by-name/wi/wikicurses/package.nix
index 4d977477108d..20aaf72be207 100644
--- a/pkgs/applications/misc/wikicurses/default.nix
+++ b/pkgs/by-name/wi/wikicurses/package.nix
@@ -1,11 +1,11 @@
 {
   lib,
   fetchFromGitHub,
-  pythonPackages,
+  python3Packages,
   installShellFiles,
 }:
 
-pythonPackages.buildPythonApplication rec {
+python3Packages.buildPythonApplication rec {
   version = "1.4";
   format = "setuptools";
   pname = "wikicurses";
@@ -26,7 +26,7 @@ pythonPackages.buildPythonApplication rec {
     installShellFiles
   ];
 
-  propagatedBuildInputs = with pythonPackages; [
+  propagatedBuildInputs = with python3Packages; [
     urwid
     beautifulsoup4
     lxml
diff --git a/pkgs/applications/networking/irc/wraith/configure.patch b/pkgs/by-name/wr/wraith/configure.patch
similarity index 100%
rename from pkgs/applications/networking/irc/wraith/configure.patch
rename to pkgs/by-name/wr/wraith/configure.patch
diff --git a/pkgs/applications/networking/irc/wraith/dlopen.patch b/pkgs/by-name/wr/wraith/dlopen.patch
similarity index 100%
rename from pkgs/applications/networking/irc/wraith/dlopen.patch
rename to pkgs/by-name/wr/wraith/dlopen.patch
diff --git a/pkgs/applications/networking/irc/wraith/default.nix b/pkgs/by-name/wr/wraith/package.nix
similarity index 92%
rename from pkgs/applications/networking/irc/wraith/default.nix
rename to pkgs/by-name/wr/wraith/package.nix
index 1a6f26aa2699..774de51eee94 100644
--- a/pkgs/applications/networking/irc/wraith/default.nix
+++ b/pkgs/by-name/wr/wraith/package.nix
@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  openssl,
+  openssl_1_1,
 }:
 
 stdenv.mkDerivation rec {
@@ -13,16 +13,16 @@ stdenv.mkDerivation rec {
     sha256 = "1h8159g6wh1hi69cnhqkgwwwa95fa6z1zrzjl219mynbf6vjjzkw";
   };
   hardeningDisable = [ "format" ];
-  buildInputs = [ openssl ];
+  buildInputs = [ openssl_1_1 ];
   patches = [
     ./configure.patch
     ./dlopen.patch
   ];
   postPatch = ''
-    substituteInPlace configure        --subst-var-by openssl.dev ${openssl.dev} \
-                                       --subst-var-by openssl-lib ${lib.getLib openssl}
-    substituteInPlace src/libssl.cc    --subst-var-by openssl ${lib.getLib openssl}
-    substituteInPlace src/libcrypto.cc --subst-var-by openssl ${lib.getLib openssl}
+    substituteInPlace configure        --subst-var-by openssl.dev ${openssl_1_1.dev} \
+                                       --subst-var-by openssl-lib ${lib.getLib openssl_1_1}
+    substituteInPlace src/libssl.cc    --subst-var-by openssl ${lib.getLib openssl_1_1}
+    substituteInPlace src/libcrypto.cc --subst-var-by openssl ${lib.getLib openssl_1_1}
   '';
   installPhase = ''
     mkdir -p $out/bin
diff --git a/pkgs/applications/graphics/sane/xsane.nix b/pkgs/by-name/xs/xsane/package.nix
similarity index 100%
rename from pkgs/applications/graphics/sane/xsane.nix
rename to pkgs/by-name/xs/xsane/package.nix
diff --git a/pkgs/applications/misc/zettlr/generic.nix b/pkgs/by-name/ze/zettlr/package.nix
similarity index 92%
rename from pkgs/applications/misc/zettlr/generic.nix
rename to pkgs/by-name/ze/zettlr/package.nix
index 76c4cf9c7463..fe3905ec75b3 100644
--- a/pkgs/applications/misc/zettlr/generic.nix
+++ b/pkgs/by-name/ze/zettlr/package.nix
@@ -1,7 +1,4 @@
 {
-  pname,
-  version,
-  hash,
   appimageTools,
   lib,
   fetchurl,
@@ -10,9 +7,12 @@
 
 # Based on https://gist.github.com/msteen/96cb7df66a359b827497c5269ccbbf94 and joplin-desktop nixpkgs.
 let
+  pname = "zettlr";
+  version = "3.4.4";
+
   src = fetchurl {
     url = "https://github.com/Zettlr/Zettlr/releases/download/v${version}/Zettlr-${version}-x86_64.appimage";
-    inherit hash;
+    hash = "sha256-ApgmHl9WoAmWl03tqv01D0W8orja25f7KZUFLhlZloQ=";
   };
   appimageContents = appimageTools.extractType2 {
     inherit pname version src;
diff --git a/pkgs/desktops/pantheon/apps/elementary-camera/default.nix b/pkgs/desktops/pantheon/apps/elementary-camera/default.nix
index 6ba592b46a67..a03bdaf89b55 100644
--- a/pkgs/desktops/pantheon/apps/elementary-camera/default.nix
+++ b/pkgs/desktops/pantheon/apps/elementary-camera/default.nix
@@ -19,13 +19,13 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-camera";
-  version = "8.0.1";
+  version = "8.0.2";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = "camera";
     rev = version;
-    sha256 = "sha256-PSUav16aU9TFX9Zb0TkqLxgn+yed86Qft0rQvbjbXtA=";
+    sha256 = "sha256-jJJhCFDo5Iw6zV6aE8JgG/sMFpUfra2j2zQ8+GjyQrk=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/desktops/pantheon/apps/elementary-videos/default.nix b/pkgs/desktops/pantheon/apps/elementary-videos/default.nix
index da3342656e73..34a3358dcff8 100644
--- a/pkgs/desktops/pantheon/apps/elementary-videos/default.nix
+++ b/pkgs/desktops/pantheon/apps/elementary-videos/default.nix
@@ -18,13 +18,13 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-videos";
-  version = "8.0.1";
+  version = "8.0.2";
 
   src = fetchFromGitHub {
     owner = "elementary";
     repo = "videos";
     rev = version;
-    hash = "sha256-3TpPgMd4dABhvnnmHHQCHDvuSdC5rWxGvaXPg20/Mrs=";
+    hash = "sha256-lvIsLjsb4HqwXDsH2krBlxmy7kJdadpjDcw+svaWV+Q=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/compilers/graalvm/default.nix b/pkgs/development/compilers/graalvm/default.nix
index 409553f9b2e4..beebfefbd0ab 100644
--- a/pkgs/development/compilers/graalvm/default.nix
+++ b/pkgs/development/compilers/graalvm/default.nix
@@ -24,7 +24,7 @@ lib.makeScope pkgs.newScope (
     truffleruby = self.callPackage ./community-edition/truffleruby { };
 
     graalvm-oracle_25-ea =
-      (self.callPackage ./graalvm-oracle { version = "25-ea-32"; }).overrideAttrs
+      (self.callPackage ./graalvm-oracle { version = "25-ea-33"; }).overrideAttrs
         (prev: {
           autoPatchelfIgnoreMissingDeps = [ "libonnxruntime.so.1" ];
         });
diff --git a/pkgs/development/compilers/graalvm/graalvm-oracle/hashes.nix b/pkgs/development/compilers/graalvm/graalvm-oracle/hashes.nix
index b593142b066b..34ab3e90724a 100644
--- a/pkgs/development/compilers/graalvm/graalvm-oracle/hashes.nix
+++ b/pkgs/development/compilers/graalvm/graalvm-oracle/hashes.nix
@@ -4,22 +4,22 @@
 # $ rg -No "(https://.+)\"" -r '$1' pkgs/development/compilers/graalvm/graalvm-oracle/hashes.nix | \
 #   parallel -k 'echo {}; nix --extra-experimental-features nix-command hash convert --hash-algo sha256 --to sri $(curl -s {}.sha256)'
 {
-  "25-ea-32" = {
+  "25-ea-33" = {
     "aarch64-linux" = {
-      hash = "sha256-JO/6VHxhd8Vetpv/iLKxNCL8wHa2VAfSIs0fiWdB4QA=";
-      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.32/graalvm-jdk-25.0.0-ea.32_linux-aarch64_bin.tar.gz";
+      hash = "sha256-VUwXu1zjjWY0K6aEpU0LhBvrz+y+H5lcspNON4Qaw6k=";
+      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.33/graalvm-jdk-25.0.0-ea.33_linux-aarch64_bin.tar.gz";
     };
     "x86_64-linux" = {
-      hash = "sha256-IevvXyhRnY/ujd3MriWULNcTYXOgt9h8bHhlJzkumjE=";
-      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.32/graalvm-jdk-25.0.0-ea.32_linux-x64_bin.tar.gz";
+      hash = "sha256-NU+tdKR9OlyE8RTVlS2w+a95ZUHBD2LDpXkqTnOL7No=";
+      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.33/graalvm-jdk-25.0.0-ea.33_linux-x64_bin.tar.gz";
     };
     "x86_64-darwin" = {
-      hash = "sha256-YhMGtXud6mer7UbSd6Eyl2d1rPKzEb6zF/NFtWLIG3E=";
-      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.32/graalvm-jdk-25.0.0-ea.32_macos-x64_bin.tar.gz";
+      hash = "sha256-TIKRKrYFjAG2BpQVp8mtbMkUlqYUpTy7R2pDH3D5Hag=";
+      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.33/graalvm-jdk-25.0.0-ea.33_macos-x64_bin.tar.gz";
     };
     "aarch64-darwin" = {
-      hash = "sha256-alNurm5ieedOi636Mnyq8BqFAyOV0dBaeTtDk4c4cPQ=";
-      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.32/graalvm-jdk-25.0.0-ea.32_macos-aarch64_bin.tar.gz";
+      hash = "sha256-hquwVXWFcGMOdmMbZHNtkYyojDKRosIi40jXOmkNlmE=";
+      url = "https://github.com/graalvm/oracle-graalvm-ea-builds/releases/download/jdk-25.0.0-ea.33/graalvm-jdk-25.0.0-ea.33_macos-aarch64_bin.tar.gz";
     };
   };
   "23" = {
diff --git a/pkgs/development/php-packages/zstd/default.nix b/pkgs/development/php-packages/zstd/default.nix
index 6924d8e1a974..9774808cf1be 100644
--- a/pkgs/development/php-packages/zstd/default.nix
+++ b/pkgs/development/php-packages/zstd/default.nix
@@ -7,7 +7,7 @@
 }:
 
 let
-  version = "0.15.0";
+  version = "0.15.1";
 in
 buildPecl {
   inherit version;
@@ -17,7 +17,7 @@ buildPecl {
     owner = "kjdev";
     repo = "php-ext-zstd";
     rev = version;
-    hash = "sha256-7Ok0Ej5U7N77Y/vXpgIp1diVSFgB9wXXGDQsKmvGxY8=";
+    hash = "sha256-Gf9/A4SmeiPGtUcTXoIU1sOzVRqIIpLAbD1QdTmBaHQ=";
   };
 
   nativeBuildInputs = [ pkg-config ];
diff --git a/pkgs/development/python-modules/add-trailing-comma/default.nix b/pkgs/development/python-modules/add-trailing-comma/default.nix
index 02bdedcaf798..9b0875773dfb 100644
--- a/pkgs/development/python-modules/add-trailing-comma/default.nix
+++ b/pkgs/development/python-modules/add-trailing-comma/default.nix
@@ -4,34 +4,38 @@
   fetchFromGitHub,
   pytestCheckHook,
   pythonOlder,
+  setuptools,
   tokenize-rt,
 }:
 
 buildPythonPackage rec {
   pname = "add-trailing-comma";
-  version = "3.1.0";
-  format = "setuptools";
+  version = "3.2.0";
+  pyproject = true;
 
-  disabled = pythonOlder "3.8";
+  disabled = pythonOlder "3.9";
 
   src = fetchFromGitHub {
     owner = "asottile";
     repo = "add-trailing-comma";
-    rev = "v${version}";
-    hash = "sha256-B+wjBy42RwabVz/6qEMGpB0JmwJ9hqSskwcNj4x/B/k=";
+    tag = "v${version}";
+    hash = "sha256-b9EHlx149NUAo9UHDZLE3BwSJY5WpxsUYi1mqz7rnHA=";
   };
 
-  propagatedBuildInputs = [ tokenize-rt ];
+  build-system = [ setuptools ];
 
-  pythonImportsCheck = [ "add_trailing_comma" ];
+  dependencies = [ tokenize-rt ];
 
   nativeCheckInputs = [ pytestCheckHook ];
 
+  pythonImportsCheck = [ "add_trailing_comma" ];
+
   meta = with lib; {
     description = "Tool (and pre-commit hook) to automatically add trailing commas to calls and literals";
-    mainProgram = "add-trailing-comma";
     homepage = "https://github.com/asottile/add-trailing-comma";
+    changelog = "https://github.com/asottile/add-trailing-comma/releases/tag/${src.tag}";
     license = licenses.mit;
     maintainers = with maintainers; [ gador ];
+    mainProgram = "add-trailing-comma";
   };
 }
diff --git a/pkgs/development/python-modules/botorch/default.nix b/pkgs/development/python-modules/botorch/default.nix
index 6bc5764d2fe9..4253117e7563 100644
--- a/pkgs/development/python-modules/botorch/default.nix
+++ b/pkgs/development/python-modules/botorch/default.nix
@@ -18,14 +18,14 @@
 
 buildPythonPackage rec {
   pname = "botorch";
-  version = "0.14.0";
+  version = "0.15.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "pytorch";
     repo = "botorch";
     tag = "v${version}";
-    hash = "sha256-IyRi5kXePnDv2q6SrXLtdltQ1/2/zQ3EBx5phtuX8sE=";
+    hash = "sha256-6hAsKIlwycZtLZn1vkcu4fR85uACA4FSkT5e/wos17A=";
   };
 
   build-system = [
diff --git a/pkgs/development/python-modules/mcp/default.nix b/pkgs/development/python-modules/mcp/default.nix
index 97ab3ceefe0c..b1d0db042282 100644
--- a/pkgs/development/python-modules/mcp/default.nix
+++ b/pkgs/development/python-modules/mcp/default.nix
@@ -40,14 +40,14 @@
 
 buildPythonPackage rec {
   pname = "mcp";
-  version = "1.12.4";
+  version = "1.13.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "modelcontextprotocol";
     repo = "python-sdk";
     tag = "v${version}";
-    hash = "sha256-FHVhufv4O7vM/9fNHyDU4L15dNLFMmoVaYd98Iw6l2o=";
+    hash = "sha256-CxrUGgQfU1R87D3ZzZCHbQBMIOJRneH6CLbHS62sCaY=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/terminaltexteffects/default.nix b/pkgs/development/python-modules/terminaltexteffects/default.nix
index e8eef5a72790..48700f6825e0 100644
--- a/pkgs/development/python-modules/terminaltexteffects/default.nix
+++ b/pkgs/development/python-modules/terminaltexteffects/default.nix
@@ -29,7 +29,7 @@ buildPythonPackage rec {
     changelog = "https://chrisbuilds.github.io/terminaltexteffects/changeblog/";
     license = licenses.mit;
     platforms = with platforms; unix;
-    maintainers = with maintainers; [ qwqawawow ];
+    maintainers = with maintainers; [ eihqnh ];
     mainProgram = "tte";
   };
 }
diff --git a/pkgs/development/tools/continuous-integration/woodpecker/common.nix b/pkgs/development/tools/continuous-integration/woodpecker/common.nix
index 9494ff61a362..036e7283cd1c 100644
--- a/pkgs/development/tools/continuous-integration/woodpecker/common.nix
+++ b/pkgs/development/tools/continuous-integration/woodpecker/common.nix
@@ -1,7 +1,7 @@
 { lib, fetchzip }:
 let
-  version = "3.8.0";
-  srcHash = "sha256-vU8lyWnXU2KnayZ863MMTMOc1/AkQ6p+uNiJOFqDNJk=";
+  version = "3.9.0";
+  srcHash = "sha256-Ymg6nJr83jt2EAv/p1B1wmZv3jvpx/3xRVRii3S1cNU=";
   # The tarball contains vendored dependencies
   vendorHash = null;
 in
diff --git a/pkgs/development/tools/misc/creduce/default.nix b/pkgs/development/tools/misc/creduce/default.nix
index 3efde95d5851..1984e22780c6 100644
--- a/pkgs/development/tools/misc/creduce/default.nix
+++ b/pkgs/development/tools/misc/creduce/default.nix
@@ -1,8 +1,7 @@
 {
   lib,
   stdenv,
-  fetchurl,
-  fetchpatch,
+  fetchFromGitHub,
   cmake,
   makeWrapper,
   llvm,
@@ -15,41 +14,23 @@
 
 stdenv.mkDerivation rec {
   pname = "creduce";
-  version = "2.10.0";
+  version = "2.10.0-unstable-2024-06-01";
 
-  src = fetchurl {
-    url = "https://embed.cs.utah.edu/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "2xwPEjln8k1iCwQM69UwAb89zwPkAPeFVqL/LhH+oGM=";
+  src = fetchFromGitHub {
+    owner = "csmith-project";
+    repo = "creduce";
+    rev = "31e855e290970cba0286e5032971509c0e7c0a80";
+    hash = "sha256-RbxFqZegsCxnUaIIA5OfTzx1wflCPeF+enQt90VwMgA=";
   };
 
-  patches = [
-    # Port to LLVM 15
-    (fetchpatch {
-      url = "https://github.com/csmith-project/creduce/commit/e507cca4ccb32585c5692d49b8d907c1051c826c.patch";
-      hash = "sha256-jO5E85AvHcjlErbUhzuQDXwQkhQsXklcTMQfWBd09OU=";
-    })
-    (fetchpatch {
-      url = "https://github.com/csmith-project/creduce/commit/8d56bee3e1d2577fc8afd2ecc03b1323d6873404.patch";
-      hash = "sha256-dRaBaJAYkvMyxKvfriOcg4D+4i6+6orZ85zws1AFx/s=";
-    })
-    # Port to LLVM 16
-    (fetchpatch {
-      url = "https://github.com/csmith-project/creduce/commit/8ab9a69caf13ce24172737e8bfd09de51a1ecb6a.patch";
-      hash = "sha256-gPNXxYHnsyUvXmC0CGtsulH2Fu/EMnDE4GdOYc0UbiQ=";
-    })
-  ];
-
-  postPatch = ''
-    substituteInPlace CMakeLists.txt \
-      --replace "-std=c++11" "-std=c++17"
-  ''
-  # On Linux, c-reduce's preferred way to reason about
-  # the cpu architecture/topology is to use 'lscpu',
-  # so let's make sure it knows where to find it:
-  + lib.optionalString stdenv.hostPlatform.isLinux ''
-    substituteInPlace creduce/creduce_utils.pm --replace \
-      lscpu ${util-linux}/bin/lscpu
-  '';
+  postPatch =
+    # On Linux, c-reduce's preferred way to reason about
+    # the cpu architecture/topology is to use 'lscpu',
+    # so let's make sure it knows where to find it:
+    lib.optionalString stdenv.hostPlatform.isLinux ''
+      substituteInPlace creduce/creduce_utils.pm --replace \
+        lscpu ${util-linux}/bin/lscpu
+    '';
 
   nativeBuildInputs = [
     cmake
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index c18a83041739..655887e016da 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -2429,10 +2429,6 @@ with pkgs;
 
   bzip2_1_1 = callPackage ../tools/compression/bzip2/1_1.nix { };
 
-  bzip3 = callPackage ../tools/compression/bzip3 {
-    stdenv = clangStdenv;
-  };
-
   davix-copy = davix.override { enableThirdPartyCopy = true; };
 
   cdist = python3Packages.callPackage ../tools/admin/cdist { };
@@ -6978,7 +6974,7 @@ with pkgs;
   credstash = with python3Packages; toPythonApplication credstash;
 
   creduce = callPackage ../development/tools/misc/creduce {
-    inherit (llvmPackages_16) llvm libclang;
+    inherit (llvmPackages_18) llvm libclang;
   };
 
   inherit (nodePackages) csslint;
@@ -15385,26 +15381,10 @@ with pkgs;
 
   hjson = with python3Packages; toPythonApplication hjson;
 
-  epkowa = callPackage ../misc/drivers/epkowa { };
-
-  utsushi = callPackage ../misc/drivers/utsushi { };
-
-  utsushi-networkscan = callPackage ../misc/drivers/utsushi/networkscan.nix { };
-
   image_optim = callPackage ../applications/graphics/image_optim { inherit (nodePackages) svgo; };
 
-  # using the new configuration style proposal which is unstable
-  jack1 = callPackage ../misc/jackaudio/jack1.nix { };
-
-  jack2 = callPackage ../misc/jackaudio { };
-
   libjack2 = jack2.override { prefix = "lib"; };
 
-  jack-example-tools = callPackage ../misc/jackaudio/tools.nix {
-    libopus = libopus.override { withCustomModes = true; };
-    jack = jack2;
-  };
-
   jack-autoconnect = libsForQt5.callPackage ../applications/audio/jack-autoconnect { };
   jack_autoconnect = jack-autoconnect;
 
@@ -15412,10 +15392,6 @@ with pkgs;
 
   kmonad = haskellPackages.kmonad.bin;
 
-  kompute = callPackage ../development/libraries/kompute {
-    fmt = fmt_10;
-  };
-
   # In general we only want keep the last three minor versions around that
   # correspond to the last three supported kubernetes versions:
   # https://kubernetes.io/docs/setup/release/version-skew-policy/#supported-versions
@@ -15446,8 +15422,6 @@ with pkgs;
 
   meilisearch_1_11 = callPackage ../by-name/me/meilisearch/package.nix { version = "1.11.3"; };
 
-  mongocxx = callPackage ../development/libraries/mongocxx/default.nix { };
-
   muse = libsForQt5.callPackage ../applications/audio/muse { };
 
   nixDependencies = recurseIntoAttrs (
@@ -15600,9 +15574,6 @@ with pkgs;
   nix-info = callPackage ../tools/nix/info { };
   nix-info-tested = nix-info.override { doCheck = true; };
 
-  nix-index-unwrapped = callPackage ../tools/package-management/nix-index { };
-  nix-index = callPackage ../tools/package-management/nix-index/wrapper.nix { };
-
   nix-linter = haskell.lib.compose.justStaticExecutables (haskellPackages.nix-linter);
 
   nix-prefetch-github = with python3Packages; toPythonApplication nix-prefetch-github;
@@ -15616,8 +15587,6 @@ with pkgs;
     nix-prefetch-scripts
     ;
 
-  nix-update-source = callPackage ../tools/package-management/nix-update-source { };
-
   nix-tree = haskell.lib.compose.justStaticExecutables (haskellPackages.nix-tree);
 
   nix-serve-ng =
@@ -15635,8 +15604,6 @@ with pkgs;
   nixpkgs-manual = callPackage ../../doc/doc-support/package.nix { };
 
   nixos-artwork = callPackage ../data/misc/nixos-artwork { };
-  nixos-icons = callPackage ../data/misc/nixos-artwork/icons.nix { };
-  nixos-grub2-theme = callPackage ../data/misc/nixos-artwork/grub2-theme.nix { };
 
   nixos-rebuild = callPackage ../os-specific/linux/nixos-rebuild { };
 
@@ -15668,9 +15635,7 @@ with pkgs;
 
   resp-app = libsForQt5.callPackage ../applications/misc/resp-app { };
 
-  pgadmin4 = callPackage ../tools/admin/pgadmin { };
-
-  pgadmin4-desktopmode = callPackage ../tools/admin/pgadmin { server-mode = false; };
+  pgadmin4-desktopmode = pgadmin4.override { server-mode = false; };
 
   philipstv = with python3Packages; toPythonApplication philipstv;
 
@@ -15693,10 +15658,6 @@ with pkgs;
 
   qtrvsim = libsForQt5.callPackage ../applications/science/computer-architecture/qtrvsim { };
 
-  romdirfs = callPackage ../tools/filesystems/romdirfs {
-    stdenv = gccStdenv;
-  };
-
   sail-riscv = callPackage ../applications/virtualization/sail-riscv {
     inherit (ocamlPackages) sail;
   };
@@ -15745,10 +15706,6 @@ with pkgs;
     callPackage ../applications/networking/cluster/terraform-providers { }
   );
 
-  terraforming = callPackage ../applications/networking/cluster/terraforming { };
-
-  terraform-landscape = callPackage ../applications/networking/cluster/terraform-landscape { };
-
   vaultenv = haskell.lib.justStaticExecutables haskellPackages.vaultenv;
 
   vaultwarden-sqlite = vaultwarden;
@@ -15771,24 +15728,8 @@ with pkgs;
 
   wacomtablet = libsForQt5.callPackage ../tools/misc/wacomtablet { };
 
-  wasmer = callPackage ../development/interpreters/wasmer {
-    llvmPackages = llvmPackages_18;
-  };
-
-  wavm = callPackage ../development/interpreters/wavm {
-    llvmPackages = llvmPackages_12;
-  };
-
-  webkit2-sharp = callPackage ../development/libraries/webkit2-sharp {
-    webkitgtk = webkitgtk_4_0;
-  };
-
   wibo = pkgsi686Linux.callPackage ../applications/emulators/wibo { };
 
-  wikicurses = callPackage ../applications/misc/wikicurses {
-    pythonPackages = python3Packages;
-  };
-
   winePackagesFor =
     wineBuild:
     lib.makeExtensible (
@@ -15849,12 +15790,6 @@ with pkgs;
     }
   );
 
-  wraith = callPackage ../applications/networking/irc/wraith {
-    openssl = openssl_1_1;
-  };
-
-  xsane = callPackage ../applications/graphics/sane/xsane.nix { };
-
   xsw = callPackage ../applications/misc/xsw {
     # Enable the next line to use this in terminal.
     # Note that it requires sixel capable terminals such as mlterm
@@ -15877,10 +15812,6 @@ with pkgs;
 
   zncModules = recurseIntoAttrs (callPackage ../applications/networking/znc/modules.nix { });
 
-  bullet = callPackage ../development/libraries/bullet { };
-
-  bullet-roboschool = callPackage ../development/libraries/bullet/roboschool-fork.nix { };
-
   dart = callPackage ../development/compilers/dart { };
 
   pub2nix = recurseIntoAttrs (callPackage ../build-support/dart/pub2nix { });
@@ -15889,8 +15820,6 @@ with pkgs;
 
   dartHooks = callPackage ../build-support/dart/build-dart-application/hooks { };
 
-  httrack = callPackage ../tools/backup/httrack { };
-
   httraqt = libsForQt5.callPackage ../tools/backup/httrack/qt.nix { };
 
   # Overriding does not work when using callPackage on discord using import instead. (https://github.com/NixOS/nixpkgs/pull/179906)
@@ -15959,10 +15888,6 @@ with pkgs;
 
   compressDrvWeb = callPackage ../build-support/compress-drv/web.nix { };
 
-  dnstracer = callPackage ../tools/networking/dnstracer {
-    inherit (darwin) libresolv;
-  };
-
   diceware = with python3Packages; toPythonApplication diceware;
 
   xml2rfc = with python3Packages; toPythonApplication xml2rfc;
@@ -16008,34 +15933,20 @@ with pkgs;
 
   xp-pen-deco-01-v2-driver = libsForQt5.xp-pen-deco-01-v2-driver;
 
-  newlib = callPackage ../development/misc/newlib { };
-
-  newlib-nano = callPackage ../development/misc/newlib {
+  newlib-nano = newlib.override {
     nanoizeNewlib = true;
   };
 
   wfuzz = with python3Packages; toPythonApplication wfuzz;
 
-  kodelife = callPackage ../applications/graphics/kodelife {
-    inherit (gst_all_1) gstreamer gst-plugins-base;
-  };
-
   sieveshell = with python3.pkgs; toPythonApplication managesieve;
 
-  gpio-utils = callPackage ../os-specific/linux/kernel/gpio-utils.nix { };
-
-  inherit (callPackage ../applications/misc/zettlr { }) zettlr;
-
   swift-corelibs-libdispatch = swiftPackages.Dispatch;
 
   aitrack = libsForQt5.callPackage ../applications/misc/aitrack { };
 
   tidal-dl = python3Packages.callPackage ../tools/audio/tidal-dl { };
 
-  tubekit = callPackage ../applications/networking/cluster/tubekit/wrapper.nix { };
-
-  tubekit-unwrapped = callPackage ../applications/networking/cluster/tubekit { };
-
   duden = python3Packages.toPythonApplication python3Packages.duden;
 
   yaziPlugins = recurseIntoAttrs (callPackage ../by-name/ya/yazi/plugins { });
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index 3cd17355e50d..1dce4e7ce77e 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -1188,6 +1188,10 @@ with self;
         --replace-fail http://cpanmetadb.plackperl.org https://cpanmetadb.plackperl.org
     '';
     propagatedBuildInputs = [ IOSocketSSL ];
+    nativeBuildInputs = lib.optional stdenv.hostPlatform.isDarwin shortenPerlShebang;
+    postInstall = lib.optionalString stdenv.hostPlatform.isDarwin ''
+      shortenPerlShebang $out/bin/cpanm
+    '';
     meta = {
       description = "Get, unpack, build and install modules from CPAN";
       homepage = "https://github.com/miyagawa/cpanminus";