diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-airshare/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-airshare/package.nix
index 9160cf770e39..5a5012750cf5 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-airshare/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-airshare/package.nix
@@ -33,7 +33,6 @@ melpaBuild {
         qrcode
       ]
       ++ ps.qrcode.optional-dependencies.pil;
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-browser/default.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-browser/default.nix
index e3053b614a4c..f804b2a65d32 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-browser/default.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-browser/default.nix
@@ -36,6 +36,12 @@ melpaBuild (finalAttrs: {
     npmHooks.npmConfigHook
   ];
 
+  postPatch = ''
+    substituteInPlace buffer.py \
+      --replace-fail "aria2_args = [\"aria2c\"]" \
+                     "aria2_args = [\"${lib.getExe aria2}\"]"
+  '';
+
   files = ''
     ("*.el"
      "*.py"
@@ -55,9 +61,6 @@ melpaBuild (finalAttrs: {
       ps: with ps; [
         pysocks
       ];
-    eafOtherDeps = [
-      aria2
-    ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-camera/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-camera/package.nix
index 13bc0a7706cc..2f4fbba74e83 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-camera/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-camera/package.nix
@@ -55,7 +55,6 @@ melpaBuild (finalAttrs: {
   passthru = {
     updateScript = nix-update-script { extraArgs = [ "--version=branch" ]; };
     eafPythonDeps = ps: [ ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-file-manager/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-file-manager/package.nix
index a338e66c610e..8d0c4ef415fc 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-file-manager/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-file-manager/package.nix
@@ -36,6 +36,14 @@ melpaBuild (finalAttrs: {
     npmHooks.npmConfigHook
   ];
 
+  postPatch = ''
+    substituteInPlace buffer.py \
+      --replace-fail "shutil.which(\"fd\")" \
+                     "shutil.which(\"${lib.getExe fd}\")" \
+      --replace-fail "return \"fd\"" \
+                     "return \"${lib.getExe fd}\""
+  '';
+
   postBuild = ''
     npm run build
   '';
@@ -62,9 +70,6 @@ melpaBuild (finalAttrs: {
         pygments
         exif
       ];
-    eafOtherDeps = [
-      fd
-    ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-git/default.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-git/default.nix
index 5b134cfc2f28..2295c988bbcb 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-git/default.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-git/default.nix
@@ -37,6 +37,16 @@ melpaBuild (finalAttrs: {
     npmHooks.npmConfigHook
   ];
 
+  postPatch = ''
+    substituteInPlace eaf-git.el \
+      --replace-fail "(defcustom eaf-git-delta-executable \"delta\"" \
+                     "(defcustom eaf-git-delta-executable \"${lib.getExe delta}\""
+
+    substituteInPlace buffer.py \
+      --replace-fail "command = \"rg '{}' {}" \
+                     "command = \"${lib.getExe ripgrep} '{}' {}"
+  '';
+
   postBuild = ''
     npm run build
   '';
@@ -65,10 +75,6 @@ melpaBuild (finalAttrs: {
         pygments
         unidiff
       ];
-    eafOtherDeps = [
-      delta
-      ripgrep
-    ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-image-viewer/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-image-viewer/package.nix
index 836e25dcbc2e..cb1f1ab14bff 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-image-viewer/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-image-viewer/package.nix
@@ -49,7 +49,6 @@ melpaBuild (finalAttrs: {
   passthru = {
     updateScript = nix-update-script { extraArgs = [ "--version=branch" ]; };
     eafPythonDeps = ps: [ ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-js-video-player/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-js-video-player/package.nix
index cfc740a74d25..519afd342d06 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-js-video-player/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-js-video-player/package.nix
@@ -55,7 +55,6 @@ melpaBuild (finalAttrs: {
   passthru = {
     updateScript = nix-update-script { extraArgs = [ "--version=branch" ]; };
     eafPythonDeps = ps: [ ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-map/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-map/package.nix
index 682f622a3ffd..e0f38b15c604 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-map/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-map/package.nix
@@ -60,7 +60,6 @@ melpaBuild (finalAttrs: {
         pycurl
         python-tsp
       ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pdf-viewer/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pdf-viewer/package.nix
index 152a573fef87..35dc987dbaae 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pdf-viewer/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pdf-viewer/package.nix
@@ -31,7 +31,6 @@ melpaBuild {
         packaging
         pymupdf
       ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pyqterminal/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pyqterminal/package.nix
index 0a2c88784518..d60787854748 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pyqterminal/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/eaf-pyqterminal/package.nix
@@ -31,7 +31,6 @@ melpaBuild {
         pyte
         psutil
       ];
-    eafOtherDeps = [ ];
   };
 
   meta = {
diff --git a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/emacs-application-framework/package.nix b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/emacs-application-framework/package.nix
index 6630a5e6b6ac..09acf5c1c472 100644
--- a/pkgs/applications/editors/emacs/elisp-packages/manual-packages/emacs-application-framework/package.nix
+++ b/pkgs/applications/editors/emacs/elisp-packages/manual-packages/emacs-application-framework/package.nix
@@ -10,7 +10,6 @@
   # Emacs dependencies
   all-the-icons,
   # Other dependencies
-  nodejs,
   wmctrl,
   xdotool,
   # Updater
@@ -22,7 +21,6 @@
 let
 
   appPythonDeps = map (item: item.eafPythonDeps) enabledApps;
-  appOtherDeps = map (item: item.eafOtherDeps) enabledApps;
 
   pythonPackageLists = [
     (
@@ -41,26 +39,15 @@ let
   pythonPkgs = ps: builtins.concatLists (map (f: f ps) pythonPackageLists);
   pythonEnv = python3.withPackages pythonPkgs;
 
-  otherPackageLists = [
-    (
-      [
-        nodejs
-        wmctrl
-      ]
-      ++ lib.optionals (lib.meta.availableOn stdenv.hostPlatform xdotool) [ xdotool ]
-    )
-  ]
-  ++ appOtherDeps;
-  otherPkgs = builtins.concatLists otherPackageLists;
+  wmctrlExe = lib.getExe wmctrl;
+  xdotoolExe = lib.optionalString (lib.meta.availableOn stdenv.hostPlatform xdotool) (
+    lib.getExe xdotool
+  );
 
   appsDrv = symlinkJoin {
     name = "emacs-application-framework-apps";
     paths = enabledApps;
   };
-  depsBin = symlinkJoin {
-    name = "emacs-application-framework-deps-bin";
-    paths = otherPkgs;
-  };
 
 in
 
@@ -84,6 +71,20 @@ melpaBuild (finalAttrs: {
     substituteInPlace eaf.el \
       --replace-fail "\"python.exe\" \"python3\"" \
                      "\"python.exe\" \"${pythonEnv.interpreter}\""
+
+    substituteInPlace eaf.el \
+      --replace-fail "(executable-find \"wmctrl\")" \
+                     "(executable-find \"${wmctrlExe}\")" \
+      --replace-fail "(shell-command-to-string \"wmctrl -m\")" \
+                     "(shell-command-to-string \"${wmctrlExe} -m\")" \
+      --replace-fail "\"wmctrl -i -a \$(wmctrl -lp | awk -vpid=\$PID '\$3==%s {print \$1; exit}')\"" \
+                     "\"${wmctrlExe} -i -a \$(${wmctrlExe} -lp | awk -vpid=\$PID '\$3==%s {print \$1; exit}')\""
+
+    substituteInPlace eaf.el \
+      --replace-fail "(executable-find \"xdotool\")" \
+                     "(executable-find \"${xdotoolExe}\")" \
+      --replace-fail "(shell-command-to-string \"xdotool getactivewindow getwindowname\")" \
+                     "(shell-command-to-string \"${xdotoolExe} getactivewindow getwindowname\")"
   '';
 
   files = ''
@@ -112,13 +113,6 @@ melpaBuild (finalAttrs: {
       cp -r $APPNATDIR/. \
             $NATDIR/
     fi
-
-    mkdir -p $out/bin/
-    for item in ${depsBin}/bin/*; do
-      # Some symbolic links point to another symbolic link
-      ln -s $(readlink -f $item) \
-            $out/bin/$(basename $item)
-    done
   '';
 
   passthru.updateScript = unstableGitUpdater { };