diff --git a/pkgs/tools/misc/h/default.nix b/pkgs/by-name/h/h/package.nix
similarity index 100%
rename from pkgs/tools/misc/h/default.nix
rename to pkgs/by-name/h/h/package.nix
diff --git a/pkgs/servers/web-apps/kavita/change-webroot.diff b/pkgs/by-name/ka/kavita/change-webroot.diff
similarity index 100%
rename from pkgs/servers/web-apps/kavita/change-webroot.diff
rename to pkgs/by-name/ka/kavita/change-webroot.diff
diff --git a/pkgs/servers/web-apps/kavita/nuget-deps.json b/pkgs/by-name/ka/kavita/nuget-deps.json
similarity index 100%
rename from pkgs/servers/web-apps/kavita/nuget-deps.json
rename to pkgs/by-name/ka/kavita/nuget-deps.json
diff --git a/pkgs/servers/web-apps/kavita/default.nix b/pkgs/by-name/ka/kavita/package.nix
similarity index 100%
rename from pkgs/servers/web-apps/kavita/default.nix
rename to pkgs/by-name/ka/kavita/package.nix
diff --git a/pkgs/servers/web-apps/kavita/update.sh b/pkgs/by-name/ka/kavita/update.sh
similarity index 100%
rename from pkgs/servers/web-apps/kavita/update.sh
rename to pkgs/by-name/ka/kavita/update.sh
diff --git a/pkgs/servers/lidarr/default.nix b/pkgs/by-name/li/lidarr/package.nix
similarity index 100%
rename from pkgs/servers/lidarr/default.nix
rename to pkgs/by-name/li/lidarr/package.nix
diff --git a/pkgs/servers/lidarr/update.sh b/pkgs/by-name/li/lidarr/update.sh
similarity index 100%
rename from pkgs/servers/lidarr/update.sh
rename to pkgs/by-name/li/lidarr/update.sh
diff --git a/pkgs/development/tools/misc/mdl/Gemfile b/pkgs/by-name/md/mdl/Gemfile
similarity index 100%
rename from pkgs/development/tools/misc/mdl/Gemfile
rename to pkgs/by-name/md/mdl/Gemfile
diff --git a/pkgs/development/tools/misc/mdl/Gemfile.lock b/pkgs/by-name/md/mdl/Gemfile.lock
similarity index 100%
rename from pkgs/development/tools/misc/mdl/Gemfile.lock
rename to pkgs/by-name/md/mdl/Gemfile.lock
diff --git a/pkgs/development/tools/misc/mdl/gemset.nix b/pkgs/by-name/md/mdl/gemset.nix
similarity index 100%
rename from pkgs/development/tools/misc/mdl/gemset.nix
rename to pkgs/by-name/md/mdl/gemset.nix
diff --git a/pkgs/development/tools/misc/mdl/default.nix b/pkgs/by-name/md/mdl/package.nix
similarity index 100%
rename from pkgs/development/tools/misc/mdl/default.nix
rename to pkgs/by-name/md/mdl/package.nix
diff --git a/pkgs/development/tools/database/pgsync/Gemfile b/pkgs/by-name/pg/pgsync/Gemfile
similarity index 100%
rename from pkgs/development/tools/database/pgsync/Gemfile
rename to pkgs/by-name/pg/pgsync/Gemfile
diff --git a/pkgs/development/tools/database/pgsync/Gemfile.lock b/pkgs/by-name/pg/pgsync/Gemfile.lock
similarity index 100%
rename from pkgs/development/tools/database/pgsync/Gemfile.lock
rename to pkgs/by-name/pg/pgsync/Gemfile.lock
diff --git a/pkgs/development/tools/database/pgsync/gemset.nix b/pkgs/by-name/pg/pgsync/gemset.nix
similarity index 100%
rename from pkgs/development/tools/database/pgsync/gemset.nix
rename to pkgs/by-name/pg/pgsync/gemset.nix
diff --git a/pkgs/development/tools/database/pgsync/default.nix b/pkgs/by-name/pg/pgsync/package.nix
similarity index 100%
rename from pkgs/development/tools/database/pgsync/default.nix
rename to pkgs/by-name/pg/pgsync/package.nix
diff --git a/pkgs/development/tools/pry/Gemfile b/pkgs/by-name/pr/pry/Gemfile
similarity index 100%
rename from pkgs/development/tools/pry/Gemfile
rename to pkgs/by-name/pr/pry/Gemfile
diff --git a/pkgs/development/tools/pry/Gemfile.lock b/pkgs/by-name/pr/pry/Gemfile.lock
similarity index 100%
rename from pkgs/development/tools/pry/Gemfile.lock
rename to pkgs/by-name/pr/pry/Gemfile.lock
diff --git a/pkgs/development/tools/pry/gemset.nix b/pkgs/by-name/pr/pry/gemset.nix
similarity index 100%
rename from pkgs/development/tools/pry/gemset.nix
rename to pkgs/by-name/pr/pry/gemset.nix
diff --git a/pkgs/development/tools/pry/default.nix b/pkgs/by-name/pr/pry/package.nix
similarity index 100%
rename from pkgs/development/tools/pry/default.nix
rename to pkgs/by-name/pr/pry/package.nix
diff --git a/pkgs/tools/misc/pws/Gemfile b/pkgs/by-name/pw/pws/Gemfile
similarity index 100%
rename from pkgs/tools/misc/pws/Gemfile
rename to pkgs/by-name/pw/pws/Gemfile
diff --git a/pkgs/tools/misc/pws/Gemfile.lock b/pkgs/by-name/pw/pws/Gemfile.lock
similarity index 100%
rename from pkgs/tools/misc/pws/Gemfile.lock
rename to pkgs/by-name/pw/pws/Gemfile.lock
diff --git a/pkgs/tools/misc/pws/gemset.nix b/pkgs/by-name/pw/pws/gemset.nix
similarity index 100%
rename from pkgs/tools/misc/pws/gemset.nix
rename to pkgs/by-name/pw/pws/gemset.nix
diff --git a/pkgs/tools/misc/pws/default.nix b/pkgs/by-name/pw/pws/package.nix
similarity index 100%
rename from pkgs/tools/misc/pws/default.nix
rename to pkgs/by-name/pw/pws/package.nix
diff --git a/pkgs/tools/networking/qcal/default.nix b/pkgs/by-name/qc/qcal/package.nix
similarity index 100%
rename from pkgs/tools/networking/qcal/default.nix
rename to pkgs/by-name/qc/qcal/package.nix
diff --git a/pkgs/tools/archivers/rar/default.nix b/pkgs/by-name/ra/rar/package.nix
similarity index 100%
rename from pkgs/tools/archivers/rar/default.nix
rename to pkgs/by-name/ra/rar/package.nix
diff --git a/pkgs/tools/archivers/rar/update.sh b/pkgs/by-name/ra/rar/update.sh
similarity index 100%
rename from pkgs/tools/archivers/rar/update.sh
rename to pkgs/by-name/ra/rar/update.sh
diff --git a/pkgs/tools/security/ronin/Gemfile b/pkgs/by-name/ro/ronin/Gemfile
similarity index 100%
rename from pkgs/tools/security/ronin/Gemfile
rename to pkgs/by-name/ro/ronin/Gemfile
diff --git a/pkgs/tools/security/ronin/Gemfile.lock b/pkgs/by-name/ro/ronin/Gemfile.lock
similarity index 100%
rename from pkgs/tools/security/ronin/Gemfile.lock
rename to pkgs/by-name/ro/ronin/Gemfile.lock
diff --git a/pkgs/tools/security/ronin/gemset.nix b/pkgs/by-name/ro/ronin/gemset.nix
similarity index 100%
rename from pkgs/tools/security/ronin/gemset.nix
rename to pkgs/by-name/ro/ronin/gemset.nix
diff --git a/pkgs/tools/security/ronin/default.nix b/pkgs/by-name/ro/ronin/package.nix
similarity index 100%
rename from pkgs/tools/security/ronin/default.nix
rename to pkgs/by-name/ro/ronin/package.nix
diff --git a/pkgs/development/tools/rover/default.nix b/pkgs/by-name/ro/rover/package.nix
similarity index 100%
rename from pkgs/development/tools/rover/default.nix
rename to pkgs/by-name/ro/rover/package.nix
diff --git a/pkgs/development/tools/rover/update.sh b/pkgs/by-name/ro/rover/update.sh
similarity index 100%
rename from pkgs/development/tools/rover/update.sh
rename to pkgs/by-name/ro/rover/update.sh
diff --git a/pkgs/development/tools/sass/Gemfile b/pkgs/by-name/sa/sass/Gemfile
similarity index 100%
rename from pkgs/development/tools/sass/Gemfile
rename to pkgs/by-name/sa/sass/Gemfile
diff --git a/pkgs/development/tools/sass/Gemfile.lock b/pkgs/by-name/sa/sass/Gemfile.lock
similarity index 100%
rename from pkgs/development/tools/sass/Gemfile.lock
rename to pkgs/by-name/sa/sass/Gemfile.lock
diff --git a/pkgs/development/tools/sass/gemset.nix b/pkgs/by-name/sa/sass/gemset.nix
similarity index 100%
rename from pkgs/development/tools/sass/gemset.nix
rename to pkgs/by-name/sa/sass/gemset.nix
diff --git a/pkgs/development/tools/sass/default.nix b/pkgs/by-name/sa/sass/package.nix
similarity index 100%
rename from pkgs/development/tools/sass/default.nix
rename to pkgs/by-name/sa/sass/package.nix
diff --git a/pkgs/applications/office/scribus/default.nix b/pkgs/by-name/sc/scribus/package.nix
similarity index 100%
rename from pkgs/applications/office/scribus/default.nix
rename to pkgs/by-name/sc/scribus/package.nix
diff --git a/pkgs/tools/misc/td/Gemfile b/pkgs/by-name/td/td/Gemfile
similarity index 100%
rename from pkgs/tools/misc/td/Gemfile
rename to pkgs/by-name/td/td/Gemfile
diff --git a/pkgs/tools/misc/td/Gemfile.lock b/pkgs/by-name/td/td/Gemfile.lock
similarity index 100%
rename from pkgs/tools/misc/td/Gemfile.lock
rename to pkgs/by-name/td/td/Gemfile.lock
diff --git a/pkgs/tools/misc/td/gemset.nix b/pkgs/by-name/td/td/gemset.nix
similarity index 100%
rename from pkgs/tools/misc/td/gemset.nix
rename to pkgs/by-name/td/td/gemset.nix
diff --git a/pkgs/tools/misc/td/default.nix b/pkgs/by-name/td/td/package.nix
similarity index 100%
rename from pkgs/tools/misc/td/default.nix
rename to pkgs/by-name/td/td/package.nix
diff --git a/pkgs/tools/misc/tremor-rs/ls.nix b/pkgs/by-name/tr/tremor-language-server/package.nix
similarity index 100%
rename from pkgs/tools/misc/tremor-rs/ls.nix
rename to pkgs/by-name/tr/tremor-language-server/package.nix
diff --git a/pkgs/tools/misc/tremor-rs/default.nix b/pkgs/by-name/tr/tremor-rs/package.nix
similarity index 100%
rename from pkgs/tools/misc/tremor-rs/default.nix
rename to pkgs/by-name/tr/tremor-rs/package.nix
diff --git a/pkgs/tools/misc/twurl/Gemfile b/pkgs/by-name/tw/twurl/Gemfile
similarity index 100%
rename from pkgs/tools/misc/twurl/Gemfile
rename to pkgs/by-name/tw/twurl/Gemfile
diff --git a/pkgs/tools/misc/twurl/Gemfile.lock b/pkgs/by-name/tw/twurl/Gemfile.lock
similarity index 100%
rename from pkgs/tools/misc/twurl/Gemfile.lock
rename to pkgs/by-name/tw/twurl/Gemfile.lock
diff --git a/pkgs/tools/misc/twurl/gemset.nix b/pkgs/by-name/tw/twurl/gemset.nix
similarity index 100%
rename from pkgs/tools/misc/twurl/gemset.nix
rename to pkgs/by-name/tw/twurl/gemset.nix
diff --git a/pkgs/tools/misc/twurl/default.nix b/pkgs/by-name/tw/twurl/package.nix
similarity index 100%
rename from pkgs/tools/misc/twurl/default.nix
rename to pkgs/by-name/tw/twurl/package.nix
diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/by-name/we/weka/package.nix
similarity index 95%
rename from pkgs/applications/science/math/weka/default.nix
rename to pkgs/by-name/we/weka/package.nix
index e7b94aa9eb61..1c5055fb1dd3 100644
--- a/pkgs/applications/science/math/weka/default.nix
+++ b/pkgs/by-name/we/weka/package.nix
@@ -2,7 +2,7 @@
   lib,
   stdenv,
   fetchurl,
-  jre,
+  openjdk11,
   unzip,
   makeWrapper,
   makeDesktopItem,
@@ -37,10 +37,10 @@ stdenv.mkDerivation rec {
     mkdir -p $out/share/icons/hicolor
     cp -Rv * $out/share/weka
 
-    makeWrapper ${jre}/bin/java $out/bin/weka \
+    makeWrapper ${openjdk11}/bin/java $out/bin/weka \
       --add-flags "-Xmx${maxMemoryAllocationPool} -jar $out/share/weka/weka.jar"
 
-    makeWrapper ${jre}/bin/java $out/bin/weka-java \
+    makeWrapper ${openjdk11}/bin/java $out/bin/weka-java \
       --add-flags "-Xmx${maxMemoryAllocationPool} -cp $out/share/weka/weka.jar"
 
     ${lib.optionalString stdenv.hostPlatform.isLinux "
diff --git a/pkgs/applications/networking/wgnord/default.nix b/pkgs/by-name/wg/wgnord/package.nix
similarity index 100%
rename from pkgs/applications/networking/wgnord/default.nix
rename to pkgs/by-name/wg/wgnord/package.nix
diff --git a/pkgs/tools/security/whatweb/Gemfile b/pkgs/by-name/wh/whatweb/Gemfile
similarity index 100%
rename from pkgs/tools/security/whatweb/Gemfile
rename to pkgs/by-name/wh/whatweb/Gemfile
diff --git a/pkgs/tools/security/whatweb/Gemfile.lock b/pkgs/by-name/wh/whatweb/Gemfile.lock
similarity index 100%
rename from pkgs/tools/security/whatweb/Gemfile.lock
rename to pkgs/by-name/wh/whatweb/Gemfile.lock
diff --git a/pkgs/tools/security/whatweb/gemset.nix b/pkgs/by-name/wh/whatweb/gemset.nix
similarity index 100%
rename from pkgs/tools/security/whatweb/gemset.nix
rename to pkgs/by-name/wh/whatweb/gemset.nix
diff --git a/pkgs/tools/security/whatweb/default.nix b/pkgs/by-name/wh/whatweb/package.nix
similarity index 100%
rename from pkgs/tools/security/whatweb/default.nix
rename to pkgs/by-name/wh/whatweb/package.nix
diff --git a/pkgs/tools/security/wpscan/Gemfile b/pkgs/by-name/wp/wpscan/Gemfile
similarity index 100%
rename from pkgs/tools/security/wpscan/Gemfile
rename to pkgs/by-name/wp/wpscan/Gemfile
diff --git a/pkgs/tools/security/wpscan/Gemfile.lock b/pkgs/by-name/wp/wpscan/Gemfile.lock
similarity index 100%
rename from pkgs/tools/security/wpscan/Gemfile.lock
rename to pkgs/by-name/wp/wpscan/Gemfile.lock
diff --git a/pkgs/tools/security/wpscan/gemset.nix b/pkgs/by-name/wp/wpscan/gemset.nix
similarity index 100%
rename from pkgs/tools/security/wpscan/gemset.nix
rename to pkgs/by-name/wp/wpscan/gemset.nix
diff --git a/pkgs/tools/security/wpscan/default.nix b/pkgs/by-name/wp/wpscan/package.nix
similarity index 100%
rename from pkgs/tools/security/wpscan/default.nix
rename to pkgs/by-name/wp/wpscan/package.nix
diff --git a/pkgs/tools/security/wpscan/update.sh b/pkgs/by-name/wp/wpscan/update.sh
similarity index 100%
rename from pkgs/tools/security/wpscan/update.sh
rename to pkgs/by-name/wp/wpscan/update.sh
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 6bc96152a7bb..bc88ce11b04f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1131,8 +1131,6 @@ with pkgs;
 
   qFlipper = libsForQt5.callPackage ../tools/misc/qflipper { };
 
-  ronin = callPackage ../tools/security/ronin { };
-
   inherit (callPackage ../development/libraries/sdbus-cpp { }) sdbus-cpp sdbus-cpp_2;
 
   sdkmanager = with python3Packages; toPythonApplication sdkmanager;
@@ -1768,8 +1766,6 @@ with pkgs;
 
   hwi = with python3Packages; toPythonApplication hwi;
 
-  kavita = callPackage ../servers/web-apps/kavita { };
-
   pass = callPackage ../tools/security/pass { };
 
   pass-nodmenu = callPackage ../tools/security/pass {
@@ -2047,8 +2043,6 @@ with pkgs;
     aspellDicts_en = aspellDicts.en;
   };
 
-  h = callPackage ../tools/misc/h { };
-
   discourse = callPackage ../servers/web-apps/discourse { };
 
   discourseAllPlugins = discourse.override {
@@ -3668,8 +3662,6 @@ with pkgs;
 
   licensee = callPackage ../tools/package-management/licensee { };
 
-  lidarr = callPackage ../servers/lidarr { };
-
   inherit
     ({
       limesuite = callPackage ../applications/radio/limesuite {
@@ -4070,8 +4062,6 @@ with pkgs;
 
   pdfium-binaries-v8 = pdfium-binaries.override { withV8 = true; };
 
-  pgsync = callPackage ../development/tools/database/pgsync { };
-
   pdsh = callPackage ../tools/networking/pdsh {
     rsh = true; # enable internal rsh implementation
     ssh = openssh;
@@ -4158,8 +4148,6 @@ with pkgs;
 
   proxmark3 = libsForQt5.callPackage ../tools/security/proxmark3/default.nix { };
 
-  pws = callPackage ../tools/misc/pws { };
-
   pycflow2dot = with python3.pkgs; toPythonApplication pycflow2dot;
 
   pyinfra = with python3Packages; toPythonApplication pyinfra;
@@ -4223,8 +4211,6 @@ with pkgs;
 
   rapidgzip = with python3Packages; toPythonApplication rapidgzip;
 
-  rar = callPackage ../tools/archivers/rar { };
-
   ratarmount = with python3Packages; toPythonApplication ratarmount;
 
   retext = qt6Packages.callPackage ../applications/editors/retext { };
@@ -4516,8 +4502,6 @@ with pkgs;
     python3Packages.callPackage ../applications/misc/twitch-chat-downloader
       { };
 
-  twurl = callPackage ../tools/misc/twurl { };
-
   ubpm = libsForQt5.callPackage ../applications/misc/ubpm { };
 
   uftraceFull = uftrace.override {
@@ -4589,8 +4573,6 @@ with pkgs;
     stdenv = clangStdenv;
   };
 
-  whatweb = callPackage ../tools/security/whatweb { };
-
   woodpecker-agent = callPackage ../development/tools/continuous-integration/woodpecker/agent.nix { };
 
   woodpecker-cli = callPackage ../development/tools/continuous-integration/woodpecker/cli.nix { };
@@ -4599,20 +4581,12 @@ with pkgs;
     callPackage ../development/tools/continuous-integration/woodpecker/server.nix
       { };
 
-  wpscan = callPackage ../tools/security/wpscan { };
-
   testdisk = libsForQt5.callPackage ../tools/system/testdisk { };
 
   testdisk-qt = testdisk.override { enableQt = true; };
 
-  td = callPackage ../tools/misc/td { };
-
   tweet-hs = haskell.lib.compose.justStaticExecutables haskellPackages.tweet-hs;
 
-  tremor-rs = callPackage ../tools/misc/tremor-rs { };
-
-  tremor-language-server = callPackage ../tools/misc/tremor-rs/ls.nix { };
-
   truecrack-cuda = truecrack.override { cudaSupport = true; };
 
   turbovnc = callPackage ../tools/admin/turbovnc {
@@ -7355,8 +7329,6 @@ with pkgs;
 
   mavproxy = python3Packages.callPackage ../applications/science/robotics/mavproxy { };
 
-  mdl = callPackage ../development/tools/misc/mdl { };
-
   meraki-cli = python3Packages.callPackage ../tools/admin/meraki-cli { };
 
   python-matter-server =
@@ -7476,8 +7448,6 @@ with pkgs;
 
   premake = premake4;
 
-  pry = callPackage ../development/tools/pry { };
-
   pycritty = with python3Packages; toPythonApplication pycritty;
 
   qtcreator = qt6Packages.callPackage ../development/tools/qtcreator {
@@ -9424,8 +9394,6 @@ with pkgs;
     };
   };
 
-  rover = callPackage ../development/tools/rover { };
-
   rshell = python3.pkgs.callPackage ../development/embedded/rshell { };
 
   schroedinger = callPackage ../development/libraries/schroedinger { };
@@ -10696,8 +10664,6 @@ with pkgs;
     elixir = elixir_1_17.override { inherit erlang; };
   };
 
-  qcal = callPackage ../tools/networking/qcal/default.nix { };
-
   rake = callPackage ../development/tools/build-managers/rake { };
 
   rethinkdb = callPackage ../servers/nosql/rethinkdb {
@@ -11189,8 +11155,6 @@ with pkgs;
 
   rfkill_udev = callPackage ../os-specific/linux/rfkill/udev.nix { };
 
-  sass = callPackage ../development/tools/sass { };
-
   sddm-astronaut = qt6Packages.callPackage ../data/themes/sddm-astronaut { };
 
   sddm-chili-theme = libsForQt5.callPackage ../data/themes/chili-sddm { };
@@ -13617,8 +13581,6 @@ with pkgs;
 
   scantailor-universal = callPackage ../applications/graphics/scantailor/universal.nix { };
 
-  scribus = callPackage ../applications/office/scribus/default.nix { };
-
   seafile-client = libsForQt5.callPackage ../applications/networking/seafile-client { };
 
   seq66 = qt5.callPackage ../applications/audio/seq66 { };
@@ -14199,8 +14161,6 @@ with pkgs;
     xwaylandSupport = false;
   };
 
-  wgnord = callPackage ../applications/networking/wgnord/default.nix { };
-
   whalebird = callPackage ../applications/misc/whalebird {
     electron = electron_36;
   };
@@ -15648,8 +15608,6 @@ with pkgs;
 
   raspa-data = callPackage ../applications/science/molecular-dynamics/raspa/data.nix { };
 
-  weka = callPackage ../applications/science/math/weka { jre = openjdk11; };
-
   yacas = libsForQt5.callPackage ../applications/science/math/yacas { };
 
   yacas-gui = yacas.override {