Wrap T3 Code apps with optional agent CLI paths

- Split base desktop/server derivations from wrapper layers
- Add optional PATH injection for codex, claudeCode, and opencode
- Update flake inputs and lock entries for nixpkgs/llm-agents

flake.lock

@@ -101,9 +101,7 @@
         "blueprint": "blueprint",
         "bun2nix": "bun2nix",
         "flake-parts": "flake-parts",
-        "nixpkgs": [
+        "nixpkgs": "nixpkgs",
-          "nixpkgs"
-        ],
         "systems": "systems",
         "treefmt-nix": "treefmt-nix"
       },
@@ -122,6 +120,22 @@
       }
     },
     "nixpkgs": {
+      "locked": {
+        "lastModified": 1776949667,
+        "narHash": "sha256-GMSVw35Q+294GlrTUKlx087E31z7KurReQ1YHSKp5iw=",
+        "owner": "NixOS",
+        "repo": "nixpkgs",
+        "rev": "01fbdeef22b76df85ea168fbfe1bfd9e63681b30",
+        "type": "github"
+      },
+      "original": {
+        "owner": "NixOS",
+        "ref": "nixpkgs-unstable",
+        "repo": "nixpkgs",
+        "type": "github"
+      }
+    },
+    "nixpkgs_2": {
       "locked": {
         "lastModified": 1776734388,
         "narHash": "sha256-vl3dkhlE5gzsItuHoEMVe+DlonsK+0836LIRDnm6MXQ=",
@@ -140,7 +154,7 @@
     "root": {
       "inputs": {
         "llm-agents": "llm-agents",
-        "nixpkgs": "nixpkgs",
+        "nixpkgs": "nixpkgs_2",
         "t3code": "t3code"
       }
     },

flake.nix

@@ -3,10 +3,7 @@
 
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-25.11";
-    llm-agents = {
+    llm-agents.url = "github:numtide/llm-agents.nix";
-      url = "github:numtide/llm-agents.nix";
-      inputs.nixpkgs.follows = "nixpkgs";
-    };
     t3code.url = "github:pingdotgg/t3code";
     t3code.flake = false;
   };

packages/common.nix

@@ -109,7 +109,11 @@ ${renderBunFilters filters}
     mkdir -p ./node_modules
     cp -R ${nodeModules}/. ./node_modules/
     chmod -R u+rwX node_modules
-    if [ ${if chmodBins then "true" else "false"} = true ] && [ -d node_modules/.bin ]; then
+    if [ ${
+      if chmodBins
+      then "true"
+      else "false"
+    } = true ] && [ -d node_modules/.bin ]; then
       chmod -R u+x node_modules/.bin
     fi
     patchShebangs node_modules

packages/node-modules-layers.nix

@@ -49,7 +49,6 @@
       export npm_config_build_from_source=true
     '';
   };
-
 in {
   inherit
     t3codeNodeModulesBase

packages/t3code-desktop/default.nix

@@ -3,6 +3,7 @@
   src,
   asar,
   stdenv,
+  symlinkJoin,
   bun,
   codex ? null,
   claudeCode ? null,
@@ -35,11 +36,7 @@
 
   pname = "t3code-desktop";
   version = desktopPackageJson.version;
-in
+  basePackage = stdenv.mkDerivation (finalAttrs: {
-  assert lib.assertMsg (!withCodex || codex != null) "withCodex requires a codex package";
-  assert lib.assertMsg (!withClaudeCode || claudeCode != null) "withClaudeCode requires a claudeCode package";
-  assert lib.assertMsg (!withOpencode || opencode != null) "withOpencode requires an opencode package";
-  stdenv.mkDerivation (finalAttrs: {
     inherit pname version;
     inherit src;
 
@@ -181,13 +178,6 @@ in
         git
         xdg-utils
       ]} \
-        ${lib.optionalString withCodex ''
-          --prefix PATH : "${lib.makeBinPath [ codex ]}" \
-        ''}${lib.optionalString withClaudeCode ''
-          --prefix PATH : "${lib.makeBinPath [ claudeCode ]}" \
-        ''}${lib.optionalString withOpencode ''
-          --prefix PATH : "${lib.makeBinPath [ opencode ]}" \
-        ''} \
         --add-flags "$out/share/${pname}/resources/app.asar"
 
       export out
@@ -205,4 +195,34 @@ in
       platforms = ["x86_64-linux"];
       sourceProvenance = with lib.sourceTypes; [fromSource];
     };
-  })
+  });
+  withAgentPath = withCodex || withClaudeCode || withOpencode;
+  agentPath = lib.makeBinPath (
+    lib.optionals withCodex [codex]
+    ++ lib.optionals withClaudeCode [claudeCode]
+    ++ lib.optionals withOpencode [opencode]
+  );
+in
+  assert lib.assertMsg (!withCodex || codex != null) "withCodex requires a codex package";
+  assert lib.assertMsg (!withClaudeCode || claudeCode != null) "withClaudeCode requires a claudeCode package";
+  assert lib.assertMsg (!withOpencode || opencode != null) "withOpencode requires an opencode package";
+    if withAgentPath
+    then
+      symlinkJoin {
+        inherit pname version;
+        name = "${pname}-${version}";
+        paths = [basePackage];
+        nativeBuildInputs = [makeWrapper];
+        postBuild = ''
+          wrapProgram "$out/bin/t3code" \
+            --prefix PATH : "${agentPath}"
+
+          rm -f "$out/share/applications/t3code.desktop"
+          install -Dm644 ${basePackage}/share/applications/t3code.desktop \
+            "$out/share/applications/t3code.desktop"
+          substituteInPlace "$out/share/applications/t3code.desktop" \
+            --replace-fail "${basePackage}/bin/t3code" "$out/bin/t3code"
+        '';
+        meta = basePackage.meta;
+      }
+    else basePackage

packages/t3code-server/default.nix

@@ -2,6 +2,7 @@
   lib,
   src,
   stdenv,
+  symlinkJoin,
   bun,
   codex ? null,
   claudeCode ? null,
@@ -28,11 +29,7 @@
 
   pname = "t3code-server";
   version = serverPackageJson.version;
-in
+  basePackage = stdenv.mkDerivation (finalAttrs: {
-  assert lib.assertMsg (!withCodex || codex != null) "withCodex requires a codex package";
-  assert lib.assertMsg (!withClaudeCode || claudeCode != null) "withClaudeCode requires a claudeCode package";
-  assert lib.assertMsg (!withOpencode || opencode != null) "withOpencode requires an opencode package";
-  stdenv.mkDerivation (finalAttrs: {
     inherit pname version;
     inherit src;
 
@@ -116,13 +113,6 @@ in
       cp -R --no-preserve=mode packages/shared "$out/libexec/t3code/packages/"
 
       makeWrapper ${lib.getExe nodejs} "$out/bin/t3" \
-        ${lib.optionalString withCodex ''
-          --prefix PATH : "${lib.makeBinPath [ codex ]}" \
-        ''}${lib.optionalString withClaudeCode ''
-          --prefix PATH : "${lib.makeBinPath [ claudeCode ]}" \
-        ''}${lib.optionalString withOpencode ''
-          --prefix PATH : "${lib.makeBinPath [ opencode ]}" \
-        ''} \
         --add-flags "$out/libexec/t3code/apps/server/dist/bin.mjs"
 
       runHook postInstall
@@ -136,4 +126,28 @@ in
       platforms = lib.platforms.unix;
       sourceProvenance = with lib.sourceTypes; [fromSource];
     };
-  })
+  });
+  withAgentPath = withCodex || withClaudeCode || withOpencode;
+  agentPath = lib.makeBinPath (
+    lib.optionals withCodex [codex]
+    ++ lib.optionals withClaudeCode [claudeCode]
+    ++ lib.optionals withOpencode [opencode]
+  );
+in
+  assert lib.assertMsg (!withCodex || codex != null) "withCodex requires a codex package";
+  assert lib.assertMsg (!withClaudeCode || claudeCode != null) "withClaudeCode requires a claudeCode package";
+  assert lib.assertMsg (!withOpencode || opencode != null) "withOpencode requires an opencode package";
+    if withAgentPath
+    then
+      symlinkJoin {
+        inherit pname version;
+        name = "${pname}-${version}";
+        paths = [basePackage];
+        nativeBuildInputs = [makeBinaryWrapper];
+        postBuild = ''
+          wrapProgram "$out/bin/t3" \
+            --prefix PATH : "${agentPath}"
+        '';
+        meta = basePackage.meta;
+      }
+    else basePackage