diff --git a/pkgs/tools/misc/grafterm/default.nix b/pkgs/by-name/gr/grafterm/package.nix
similarity index 100%
rename from pkgs/tools/misc/grafterm/default.nix
rename to pkgs/by-name/gr/grafterm/package.nix
diff --git a/pkgs/development/tools/konf/default.nix b/pkgs/by-name/ko/konf/package.nix
similarity index 100%
rename from pkgs/development/tools/konf/default.nix
rename to pkgs/by-name/ko/konf/package.nix
diff --git a/pkgs/tools/misc/octosql/default.nix b/pkgs/by-name/oc/octosql/package.nix
similarity index 100%
rename from pkgs/tools/misc/octosql/default.nix
rename to pkgs/by-name/oc/octosql/package.nix
diff --git a/pkgs/tools/misc/promql-cli/default.nix b/pkgs/by-name/pr/promql-cli/package.nix
similarity index 100%
rename from pkgs/tools/misc/promql-cli/default.nix
rename to pkgs/by-name/pr/promql-cli/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index df3c7b428dac..78be565db511 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -787,8 +787,6 @@ with pkgs;
 
   octosuite = callPackage ../tools/security/octosuite { };
 
-  octosql = callPackage ../tools/misc/octosql { };
-
   onesixtyone = callPackage ../tools/security/onesixtyone { };
 
   oletools = with python3.pkgs; toPythonApplication oletools;
@@ -8495,8 +8493,6 @@ with pkgs;
 
   gql = callPackage ../applications/version-management/gql { };
 
-  grafterm = callPackage ../tools/misc/grafterm { };
-
   gradience = callPackage ../applications/misc/gradience { };
 
   grafx2 = callPackage ../applications/graphics/grafx2 { };
@@ -17051,8 +17047,6 @@ with pkgs;
 
   kona = callPackage ../development/interpreters/kona { };
 
-  konf = callPackage ../development/tools/konf { };
-
   lambda-lisp = callPackage ../development/interpreters/lambda-lisp { };
   lambda-lisp-blc = lambda-lisp;
 
@@ -26074,8 +26068,6 @@ with pkgs;
 
   liquibase_redshift_extension = callPackage ../development/java-modules/liquibase_redshift_extension { };
 
-  promql-cli = callPackage ../tools/misc/promql-cli { };
-
   prom2json = callPackage ../servers/monitoring/prometheus/prom2json.nix { };
   prometheus = callPackage ../servers/monitoring/prometheus { };
   prometheus-alertmanager = callPackage ../servers/monitoring/prometheus/alertmanager.nix { };