diff --git a/pkgs/by-name/bl/blender/package.nix b/pkgs/by-name/bl/blender/package.nix
index c5ca3d1f982f7..1cedbfce2aac8 100644
--- a/pkgs/by-name/bl/blender/package.nix
+++ b/pkgs/by-name/bl/blender/package.nix
@@ -16,7 +16,7 @@
   embree,
   fetchzip,
   fetchFromGitHub,
-  ffmpeg_7,
+  ffmpeg,
   fftw,
   fftwFloat,
   freetype,
@@ -234,7 +234,7 @@ stdenv'.mkDerivation (finalAttrs: {
   buildInputs = [
     alembic
     boost
-    ffmpeg_7
+    ffmpeg
     fftw
     fftwFloat
     freetype
diff --git a/pkgs/by-name/bl/blender/pins.nix b/pkgs/by-name/bl/blender/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/bl/blender/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/ch/chiaki/package.nix b/pkgs/by-name/ch/chiaki/package.nix
index 39720c826f2e6..76bba18cd7c4a 100644
--- a/pkgs/by-name/ch/chiaki/package.nix
+++ b/pkgs/by-name/ch/chiaki/package.nix
@@ -4,7 +4,7 @@
   fetchgit,
   cmake,
   pkg-config,
-  ffmpeg_7,
+  ffmpeg,
   libopus,
   SDL2,
   libevdev,
@@ -37,7 +37,7 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   buildInputs = [
-    ffmpeg_7 # needs avcodec_close which was removed in ffmpeg 8
+    ffmpeg
     libopus
     libsForQt5.qtbase
     libsForQt5.qtmultimedia
diff --git a/pkgs/by-name/ch/chiaki/pins.nix b/pkgs/by-name/ch/chiaki/pins.nix
new file mode 100644
index 0000000000000..f3c1fea81ecdf
--- /dev/null
+++ b/pkgs/by-name/ch/chiaki/pins.nix
@@ -0,0 +1,5 @@
+{ ffmpeg_7 }:
+{
+  # needs avcodec_close which was removed in ffmpeg 8
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/dj/djv/package.nix b/pkgs/by-name/dj/djv/package.nix
index 2a861f28d7c80..9cc1ae9d13174 100644
--- a/pkgs/by-name/dj/djv/package.nix
+++ b/pkgs/by-name/dj/djv/package.nix
@@ -6,7 +6,7 @@
   pkg-config,
   bzip2,
   feather-tk,
-  ffmpeg_7,
+  ffmpeg,
   freetype,
   glfw,
   imath,
@@ -56,7 +56,7 @@ stdenv.mkDerivation (finalAttrs: {
   buildInputs = [
     bzip2
     feather-tk
-    ffmpeg_7
+    ffmpeg
     freetype
     glfw
     imath
diff --git a/pkgs/by-name/dj/djv/pins.nix b/pkgs/by-name/dj/djv/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/dj/djv/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/ml/mlt/package.nix b/pkgs/by-name/ml/mlt/package.nix
index ae965a28077cf..3b85c79707576 100644
--- a/pkgs/by-name/ml/mlt/package.nix
+++ b/pkgs/by-name/ml/mlt/package.nix
@@ -6,7 +6,7 @@
   cmake,
   pkg-config,
   which,
-  ffmpeg_7,
+  ffmpeg,
   fftw,
   frei0r,
   libdv,
@@ -71,8 +71,8 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    (opencv4.override { inherit ffmpeg_7; })
-    ffmpeg_7
+    (opencv4.override { ffmpeg_7 = ffmpeg; })
+    ffmpeg
     fftw
     frei0r
     libdv
@@ -137,7 +137,7 @@ stdenv.mkDerivation rec {
   '';
 
   passthru = {
-    ffmpeg = ffmpeg_7;
+    ffmpeg = ffmpeg;
   };
 
   passthru.updateScript = gitUpdater {
diff --git a/pkgs/by-name/ml/mlt/pins.nix b/pkgs/by-name/ml/mlt/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/ml/mlt/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/re/retroarch-bare/package.nix b/pkgs/by-name/re/retroarch-bare/package.nix
index 266ac84cbdf91..44fa61e1b9475 100644
--- a/pkgs/by-name/re/retroarch-bare/package.nix
+++ b/pkgs/by-name/re/retroarch-bare/package.nix
@@ -5,7 +5,7 @@
   alsa-lib,
   dbus,
   fetchFromGitHub,
-  ffmpeg_7,
+  ffmpeg,
   flac,
   freetype,
   gamemode,
@@ -75,7 +75,7 @@ stdenv.mkDerivation rec {
   ++ lib.optional (runtimeLibs != [ ]) makeBinaryWrapper;
 
   buildInputs = [
-    ffmpeg_7
+    ffmpeg
     flac
     freetype
     libGL
diff --git a/pkgs/by-name/re/retroarch-bare/pins.nix b/pkgs/by-name/re/retroarch-bare/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/re/retroarch-bare/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/rp/rpcs3/package.nix b/pkgs/by-name/rp/rpcs3/package.nix
index 4fea7834c994a..109f71454fe25 100644
--- a/pkgs/by-name/rp/rpcs3/package.nix
+++ b/pkgs/by-name/rp/rpcs3/package.nix
@@ -14,7 +14,7 @@
   vulkan-loader,
   libpng,
   libSM,
-  ffmpeg_7,
+  ffmpeg,
   libevdev,
   libusb1,
   zlib,
@@ -120,7 +120,7 @@ stdenv.mkDerivation (finalAttrs: {
     vulkan-headers
     vulkan-loader
     libpng
-    ffmpeg_7
+    ffmpeg
     libevdev
     zlib
     libusb1
diff --git a/pkgs/by-name/rp/rpcs3/pins.nix b/pkgs/by-name/rp/rpcs3/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/rp/rpcs3/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/ru/rustdesk-flutter/package.nix b/pkgs/by-name/ru/rustdesk-flutter/package.nix
index 1544b0e838f05..05459b33fc5cb 100644
--- a/pkgs/by-name/ru/rustdesk-flutter/package.nix
+++ b/pkgs/by-name/ru/rustdesk-flutter/package.nix
@@ -5,7 +5,7 @@
   copyDesktopItems,
   fetchFromGitHub,
   flutter329,
-  ffmpeg_7,
+  ffmpeg,
   gst_all_1,
   fuse3,
   libXtst,
@@ -119,7 +119,7 @@ flutter329.buildFlutterApplication rec {
   ];
 
   buildInputs = [
-    ffmpeg_7
+    ffmpeg
     fuse3
     gst_all_1.gst-plugins-base
     gst_all_1.gstreamer
diff --git a/pkgs/by-name/ru/rustdesk-flutter/pins.nix b/pkgs/by-name/ru/rustdesk-flutter/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/ru/rustdesk-flutter/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/te/tenacity/package.nix b/pkgs/by-name/te/tenacity/package.nix
index 3636dc9342eee..f98250ed65f52 100644
--- a/pkgs/by-name/te/tenacity/package.nix
+++ b/pkgs/by-name/te/tenacity/package.nix
@@ -31,7 +31,7 @@
   expat,
   libid3tag,
   libopus,
-  ffmpeg_7,
+  ffmpeg,
   soundtouch,
   pcre,
   portaudio,
@@ -76,7 +76,7 @@ stdenv.mkDerivation (finalAttrs: {
     # looking only in a few specific directories.
     # Make sure it searches for our version of ffmpeg in the nix store.
     substituteInPlace libraries/lib-ffmpeg-support/FFmpegFunctions.cpp \
-      --replace-fail /usr/local/lib/tenacity ${lib.getLib ffmpeg_7}/lib
+      --replace-fail /usr/local/lib/tenacity ${lib.getLib ffmpeg}/lib
   '';
 
   postInstall = lib.optionalString stdenv.hostPlatform.isDarwin ''
@@ -130,7 +130,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   buildInputs = [
     expat
-    ffmpeg_7
+    ffmpeg
     file
     flac
     glib
diff --git a/pkgs/by-name/te/tenacity/pins.nix b/pkgs/by-name/te/tenacity/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/te/tenacity/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/tl/tlrender/package.nix b/pkgs/by-name/tl/tlrender/package.nix
index 6704c59925652..81893619f5af7 100644
--- a/pkgs/by-name/tl/tlrender/package.nix
+++ b/pkgs/by-name/tl/tlrender/package.nix
@@ -7,7 +7,7 @@
 
   bzip2,
   feather-tk,
-  ffmpeg_7,
+  ffmpeg,
   freetype,
   glfw,
   imath,
@@ -112,7 +112,7 @@ stdenv.mkDerivation (finalAttrs: {
   ++ lib.optionals enableTiff [ libtiff ]
   ++ lib.optionals enablePng [ libpng ]
   ++ lib.optionals enableOpenexr [ openexr ]
-  ++ lib.optionals enableFfmpeg [ ffmpeg_7 ]
+  ++ lib.optionals enableFfmpeg [ ffmpeg ]
   ++ lib.optionals enableUsd [ openusd ];
 
   cmakeFlags = [
diff --git a/pkgs/by-name/tl/tlrender/pins.nix b/pkgs/by-name/tl/tlrender/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/tl/tlrender/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/by-name/yt/ytdl-sub/package.nix b/pkgs/by-name/yt/ytdl-sub/package.nix
index 2815ce3114d6a..2578b4b3fcd3d 100644
--- a/pkgs/by-name/yt/ytdl-sub/package.nix
+++ b/pkgs/by-name/yt/ytdl-sub/package.nix
@@ -1,7 +1,7 @@
 {
   python3Packages,
   fetchFromGitHub,
-  ffmpeg_7,
+  ffmpeg,
   lib,
   versionCheckHook,
 }:
@@ -38,8 +38,8 @@ python3Packages.buildPythonApplication rec {
   ];
 
   makeWrapperArgs = [
-    "--set YTDL_SUB_FFMPEG_PATH ${lib.getExe' ffmpeg_7 "ffmpeg"}"
-    "--set YTDL_SUB_FFPROBE_PATH ${lib.getExe' ffmpeg_7 "ffprobe"}"
+    "--set YTDL_SUB_FFMPEG_PATH ${lib.getExe' ffmpeg "ffmpeg"}"
+    "--set YTDL_SUB_FFPROBE_PATH ${lib.getExe' ffmpeg "ffprobe"}"
   ];
 
   nativeCheckInputs = [
@@ -49,8 +49,8 @@ python3Packages.buildPythonApplication rec {
   versionCheckProgramArg = "--version";
 
   env = {
-    YTDL_SUB_FFMPEG_PATH = "${lib.getExe' ffmpeg_7 "ffmpeg"}";
-    YTDL_SUB_FFPROBE_PATH = "${lib.getExe' ffmpeg_7 "ffprobe"}";
+    YTDL_SUB_FFMPEG_PATH = "${lib.getExe' ffmpeg "ffmpeg"}";
+    YTDL_SUB_FFPROBE_PATH = "${lib.getExe' ffmpeg "ffprobe"}";
   };
 
   disabledTests = [
diff --git a/pkgs/by-name/yt/ytdl-sub/pins.nix b/pkgs/by-name/yt/ytdl-sub/pins.nix
new file mode 100644
index 0000000000000..87892a11e15e4
--- /dev/null
+++ b/pkgs/by-name/yt/ytdl-sub/pins.nix
@@ -0,0 +1,4 @@
+{ ffmpeg_7 }:
+{
+  ffmpeg = ffmpeg_7;
+}
diff --git a/pkgs/top-level/by-name-overlay.nix b/pkgs/top-level/by-name-overlay.nix
index e6fe5b7215560..69bedf15348b0 100644
--- a/pkgs/top-level/by-name-overlay.nix
+++ b/pkgs/top-level/by-name-overlay.nix
@@ -19,7 +19,7 @@ let
     mergeAttrsList
     ;
 
-  # Package files for a single shard
+  # Package directories for a single shard
   # Type: String -> String -> AttrsOf Path
   namesForShard =
     shard: type:
@@ -32,23 +32,23 @@ let
       # Additionally in either of those alternatives, we would have to duplicate the hardcoding of "README.md"
       { }
     else
-      mapAttrs (name: _: baseDirectory + "/${shard}/${name}/package.nix") (
-        readDir (baseDirectory + "/${shard}")
-      );
+      mapAttrs (name: _: baseDirectory + "/${shard}/${name}") (readDir (baseDirectory + "/${shard}"));
 
   # The attribute set mapping names to the package files defining them
   # This is defined up here in order to allow reuse of the value (it's kind of expensive to compute)
   # if the overlay has to be applied multiple times
-  packageFiles = mergeAttrsList (mapAttrsToList namesForShard (readDir baseDirectory));
+  packageDirectories = mergeAttrsList (mapAttrsToList namesForShard (readDir baseDirectory));
 in
-self: super:
-{
-  # This attribute is necessary to allow CI to ensure that all packages defined in `pkgs/by-name`
-  # don't have an overriding definition in `all-packages.nix` with an empty (`{ }`) second `callPackage` argument.
-  # It achieves that with an overlay that modifies both `callPackage` and this attribute to signal whether `callPackage` is used
-  # and whether it's defined by this file here or `all-packages.nix`.
-  # TODO: This can be removed once `pkgs/by-name` can handle custom `callPackage` arguments without `all-packages.nix` (or any other way of achieving the same result).
-  # Because at that point the code in ./stage.nix can be changed to not allow definitions in `all-packages.nix` to override ones from `pkgs/by-name` anymore and throw an error if that happens instead.
-  _internalCallByNamePackageFile = file: self.callPackage file { };
-}
-// mapAttrs (name: self._internalCallByNamePackageFile) packageFiles
+final: prev:
+mapAttrs (
+  _: packageDirectory:
+  if lib.pathExists (packageDirectory + "/pins.nix") then
+    final.callPackage (packageDirectory + "/package.nix") (
+      lib.removeAttrs (final.callPackage (packageDirectory + "/pins.nix") { }) [
+        "override"
+        "overrideDerivation"
+      ]
+    )
+  else
+    final.callPackage (packageDirectory + "/package.nix") { }
+) packageDirectories