diff --git a/pkgs/applications/misc/bazecor/10-dygma.rules b/pkgs/by-name/ba/bazecor/10-dygma.rules
similarity index 100%
rename from pkgs/applications/misc/bazecor/10-dygma.rules
rename to pkgs/by-name/ba/bazecor/10-dygma.rules
diff --git a/pkgs/applications/misc/bazecor/default.nix b/pkgs/by-name/ba/bazecor/package.nix
similarity index 100%
rename from pkgs/applications/misc/bazecor/default.nix
rename to pkgs/by-name/ba/bazecor/package.nix
diff --git a/pkgs/development/tools/cddl/Gemfile b/pkgs/by-name/cd/cddl/Gemfile
similarity index 100%
rename from pkgs/development/tools/cddl/Gemfile
rename to pkgs/by-name/cd/cddl/Gemfile
diff --git a/pkgs/development/tools/cddl/Gemfile.lock b/pkgs/by-name/cd/cddl/Gemfile.lock
similarity index 100%
rename from pkgs/development/tools/cddl/Gemfile.lock
rename to pkgs/by-name/cd/cddl/Gemfile.lock
diff --git a/pkgs/development/tools/cddl/gemset.nix b/pkgs/by-name/cd/cddl/gemset.nix
similarity index 100%
rename from pkgs/development/tools/cddl/gemset.nix
rename to pkgs/by-name/cd/cddl/gemset.nix
diff --git a/pkgs/development/tools/cddl/default.nix b/pkgs/by-name/cd/cddl/package.nix
similarity index 100%
rename from pkgs/development/tools/cddl/default.nix
rename to pkgs/by-name/cd/cddl/package.nix
diff --git a/pkgs/tools/misc/gh-actions-cache/default.nix b/pkgs/by-name/gh/gh-actions-cache/package.nix
similarity index 100%
rename from pkgs/tools/misc/gh-actions-cache/default.nix
rename to pkgs/by-name/gh/gh-actions-cache/package.nix
diff --git a/pkgs/tools/misc/gh-dash/default.nix b/pkgs/by-name/gh/gh-dash/package.nix
similarity index 100%
rename from pkgs/tools/misc/gh-dash/default.nix
rename to pkgs/by-name/gh/gh-dash/package.nix
diff --git a/pkgs/tools/misc/gh-markdown-preview/default.nix b/pkgs/by-name/gh/gh-markdown-preview/package.nix
similarity index 100%
rename from pkgs/tools/misc/gh-markdown-preview/default.nix
rename to pkgs/by-name/gh/gh-markdown-preview/package.nix
diff --git a/pkgs/development/libraries/science/math/latte-integrale/default.nix b/pkgs/by-name/la/latte-integrale/package.nix
similarity index 100%
rename from pkgs/development/libraries/science/math/latte-integrale/default.nix
rename to pkgs/by-name/la/latte-integrale/package.nix
diff --git a/pkgs/applications/version-management/scriv/default.nix b/pkgs/by-name/sc/scriv/package.nix
similarity index 100%
rename from pkgs/applications/version-management/scriv/default.nix
rename to pkgs/by-name/sc/scriv/package.nix
diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/by-name/ta/tandem-aligner/package.nix
similarity index 100%
rename from pkgs/applications/science/biology/tandem-aligner/default.nix
rename to pkgs/by-name/ta/tandem-aligner/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1a4bc3a96335..150c5785dcc0 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -334,8 +334,6 @@ with pkgs;
 
   bakelite = callPackage ../tools/backup/bakelite { };
 
-  bazecor = callPackage ../applications/misc/bazecor { };
-
   bearer = callPackage ../development/tools/bearer { };
 
   benthos = callPackage ../development/tools/benthos { };
@@ -1785,16 +1783,10 @@ with pkgs;
 
   gfshare = callPackage ../tools/security/gfshare { };
 
-  gh-actions-cache = callPackage ../tools/misc/gh-actions-cache { };
-
   gh-cal = callPackage ../tools/misc/gh-cal {
     inherit (darwin.apple_sdk.frameworks) Security;
   };
 
-  gh-dash = callPackage ../tools/misc/gh-dash { };
-
-  gh-markdown-preview = callPackage ../tools/misc/gh-markdown-preview { };
-
   ghostie = callPackage ../tools/misc/ghostie { };
 
   glooctl = callPackage ../applications/networking/cluster/glooctl { };
@@ -2991,8 +2983,6 @@ with pkgs;
 
   sakura = callPackage ../applications/terminal-emulators/sakura { };
 
-  scriv = callPackage ../applications/version-management/scriv { };
-
   st = callPackage ../applications/terminal-emulators/st {
     conf = config.st.conf or null;
     patches = config.st.patches or [];
@@ -4462,8 +4452,6 @@ with pkgs;
 
   cbftp = callPackage ../tools/networking/cbftp { };
 
-  cddl = callPackage ../development/tools/cddl { };
-
   cedille = callPackage ../applications/science/logic/cedille
                           { inherit (haskellPackages) alex happy Agda ghcWithPackages;
                           };
@@ -37278,8 +37266,6 @@ with pkgs;
 
   svaba = callPackage ../applications/science/biology/svaba { };
 
-  tandem-aligner = callPackage ../applications/science/biology/tandem-aligner { };
-
   tebreak = callPackage ../applications/science/biology/tebreak { };
 
   treemix = callPackage ../applications/science/biology/treemix { };
@@ -37414,8 +37400,6 @@ with pkgs;
 
   rankwidth = callPackage ../development/libraries/science/math/rankwidth { };
 
-  latte-integrale = callPackage ../development/libraries/science/math/latte-integrale { };
-
   lcalc = callPackage ../development/libraries/science/math/lcalc { };
 
   lrcalc = callPackage ../applications/science/math/lrcalc { };