From 4fcef56c15326af5e419fae4e059bb099c6c3800 Mon Sep 17 00:00:00 2001
From: Austin Horstman <khaneliman12@gmail.com>
Date: Wed, 18 Mar 2026 16:57:42 -0500
Subject: [PATCH] claude-code: load MCP config via plugin dir

Claude Code rejects `--mcp-config` once the Home Manager wrapper injects
it around subcommands, which breaks commands like `claude mcp list`.
Claude Code 2.1.76 fixed `--plugin-dir` so it no longer consumes
following subcommands, so use that path for the generated MCP config
instead.

Generate a plugin directory with a manifest and `.mcp.json`, wrap
`claude` with `--plugin-dir` before user arguments, and snapshot that
wrapper directly in the tests. Keep the existing LSP support in the
generated plugin directory as well, and add coverage for the combined
MCP+LSP case plus the MCP integration merge path.

Signed-off-by: Austin Horstman <khaneliman12@gmail.com>
---
 modules/programs/claude-code.nix              | 56 ++++++-------
 .../modules/programs/claude-code/default.nix  |  1 +
 .../claude-code/expected-lsp-plugin.json      | 21 +++++
 .../programs/claude-code/expected-lsp-wrapper |  4 +-
 .../claude-code/expected-mcp-plugin.json      | 36 +++++++++
 .../programs/claude-code/expected-mcp-wrapper |  4 +-
 .../claude-code/expected-plugin-manifest.json |  3 +
 tests/modules/programs/claude-code/lsp.nix    | 11 ++-
 .../programs/claude-code/mcp-integration.nix  | 16 +++-
 .../modules/programs/claude-code/mcp-lsp.nix  | 81 +++++++++++++++++++
 tests/modules/programs/claude-code/mcp.nix    | 11 ++-
 11 files changed, 205 insertions(+), 39 deletions(-)
 create mode 100644 tests/modules/programs/claude-code/expected-lsp-plugin.json
 create mode 100644 tests/modules/programs/claude-code/expected-mcp-plugin.json
 create mode 100644 tests/modules/programs/claude-code/expected-plugin-manifest.json
 create mode 100644 tests/modules/programs/claude-code/mcp-lsp.nix

diff --git a/modules/programs/claude-code.nix b/modules/programs/claude-code.nix
index ceadba99..9700416e 100644
--- a/modules/programs/claude-code.nix
+++ b/modules/programs/claude-code.nix
@@ -469,39 +469,39 @@ in
     programs.claude-code.finalPackage =
       let
         mergedMcpServers = transformedMcpServers // cfg.mcpServers;
-        makeWrapperArgs = lib.flatten (
-          lib.filter (x: x != [ ]) [
-            (lib.optional (cfg.mcpServers != { } || transformedMcpServers != { }) [
-              "--append-flags"
-              "--mcp-config ${
-                jsonFormat.generate "claude-code-mcp-config.json" { mcpServers = mergedMcpServers; }
-              }"
-            ])
-            (lib.optional (cfg.lspServers != { }) [
-              "--append-flags"
-              "--plugin-dir ${
-                pkgs.runCommand "claude-code-lsp-plugin" { } ''
-                  install -Dm644 ${
-                    jsonFormat.generate "claude-code-lsp-plugin.json" {
-                      name = "claude-code-lsp";
-                      lspServers = cfg.lspServers;
-                    }
-                  } $out/.claude-plugin/plugin.json
-                ''
-              }"
-            ])
-          ]
-        );
-
-        hasWrapperArgs = makeWrapperArgs != [ ];
+        hasMcpServers = mergedMcpServers != { };
+        hasLspServers = cfg.lspServers != { };
+        pluginDir =
+          if hasMcpServers || hasLspServers then
+            pkgs.runCommand "claude-code-hm-plugin" { } ''
+              install -Dm644 ${
+                jsonFormat.generate "claude-code-plugin.json" {
+                  name = "claude-code-home-manager";
+                }
+              } $out/.claude-plugin/plugin.json
+              ${lib.optionalString hasMcpServers ''
+                install -Dm644 ${
+                  jsonFormat.generate "claude-code-mcp.json" { mcpServers = mergedMcpServers; }
+                } $out/.mcp.json
+              ''}
+              ${lib.optionalString hasLspServers ''
+                install -Dm644 ${jsonFormat.generate "claude-code-lsp.json" cfg.lspServers} $out/.lsp.json
+              ''}
+            ''
+          else
+            null;
       in
-      if hasWrapperArgs then
+      if pluginDir != null then
         pkgs.symlinkJoin {
           name = "claude-code";
           paths = [ cfg.package ];
-          nativeBuildInputs = [ pkgs.makeWrapper ];
           postBuild = ''
-            wrapProgram $out/bin/claude ${lib.escapeShellArgs makeWrapperArgs}
+            mv $out/bin/claude $out/bin/.claude-wrapped
+            cat > $out/bin/claude <<EOF
+            #! ${pkgs.bash}/bin/bash -e
+            exec -a "\$0" "$out/bin/.claude-wrapped" --plugin-dir ${pluginDir} "\$@"
+            EOF
+            chmod +x $out/bin/claude
           '';
           inherit (cfg.package) meta;
         }
diff --git a/tests/modules/programs/claude-code/default.nix b/tests/modules/programs/claude-code/default.nix
index acfaf6ef..5fd41a57 100644
--- a/tests/modules/programs/claude-code/default.nix
+++ b/tests/modules/programs/claude-code/default.nix
@@ -3,6 +3,7 @@
   claude-code-full-config = ./full-config.nix;
   claude-code-lsp = ./lsp.nix;
   claude-code-mcp = ./mcp.nix;
+  claude-code-mcp-lsp = ./mcp-lsp.nix;
   claude-code-mcp-integration = ./mcp-integration.nix;
   claude-code-assertion = ./assertion.nix;
   claude-code-memory-management = ./memory-management.nix;
diff --git a/tests/modules/programs/claude-code/expected-lsp-plugin.json b/tests/modules/programs/claude-code/expected-lsp-plugin.json
new file mode 100644
index 00000000..95816bb9
--- /dev/null
+++ b/tests/modules/programs/claude-code/expected-lsp-plugin.json
@@ -0,0 +1,21 @@
+{
+  "go": {
+    "args": [
+      "serve"
+    ],
+    "command": "gopls",
+    "extensionToLanguage": {
+      ".go": "go"
+    }
+  },
+  "typescript": {
+    "args": [
+      "--stdio"
+    ],
+    "command": "typescript-language-server",
+    "extensionToLanguage": {
+      ".ts": "typescript",
+      ".tsx": "typescriptreact"
+    }
+  }
+}
diff --git a/tests/modules/programs/claude-code/expected-lsp-wrapper b/tests/modules/programs/claude-code/expected-lsp-wrapper
index aaadf0c3..189bafb0 100644
--- a/tests/modules/programs/claude-code/expected-lsp-wrapper
+++ b/tests/modules/programs/claude-code/expected-lsp-wrapper
@@ -1,2 +1,2 @@
-#! /nix/store/00000000000000000000000000000000-bash/bin/bash -e
-exec -a "$0" "/nix/store/00000000000000000000000000000000-claude-code/bin/.claude-wrapped"  "$@"  --plugin-dir /nix/store/00000000000000000000000000000000-claude-code-lsp-plugin
+#! @bash-interactive@/bin/bash -e
+exec -a "$0" "/nix/store/00000000000000000000000000000000-claude-code/bin/.claude-wrapped" --plugin-dir /nix/store/00000000000000000000000000000000-claude-code-hm-plugin "$@"
diff --git a/tests/modules/programs/claude-code/expected-mcp-plugin.json b/tests/modules/programs/claude-code/expected-mcp-plugin.json
new file mode 100644
index 00000000..72d5eb31
--- /dev/null
+++ b/tests/modules/programs/claude-code/expected-mcp-plugin.json
@@ -0,0 +1,36 @@
+{
+  "mcpServers": {
+    "customTransport": {
+      "customOption": "value",
+      "timeout": 5000,
+      "type": "websocket",
+      "url": "wss://example.com/mcp"
+    },
+    "database": {
+      "args": [
+        "-y",
+        "@bytebase/dbhub",
+        "--dsn",
+        "postgresql://user:pass@localhost:5432/db"
+      ],
+      "command": "npx",
+      "env": {
+        "DATABASE_URL": "postgresql://user:pass@localhost:5432/db"
+      },
+      "type": "stdio"
+    },
+    "filesystem": {
+      "args": [
+        "-y",
+        "@modelcontextprotocol/server-filesystem",
+        "/tmp"
+      ],
+      "command": "npx",
+      "type": "stdio"
+    },
+    "github": {
+      "type": "http",
+      "url": "https://api.githubcopilot.com/mcp/"
+    }
+  }
+}
diff --git a/tests/modules/programs/claude-code/expected-mcp-wrapper b/tests/modules/programs/claude-code/expected-mcp-wrapper
index 7a582173..189bafb0 100644
--- a/tests/modules/programs/claude-code/expected-mcp-wrapper
+++ b/tests/modules/programs/claude-code/expected-mcp-wrapper
@@ -1,2 +1,2 @@
-#! /nix/store/00000000000000000000000000000000-bash/bin/bash -e
-exec -a "$0" "/nix/store/00000000000000000000000000000000-claude-code/bin/.claude-wrapped"  "$@"  --mcp-config /nix/store/00000000000000000000000000000000-claude-code-mcp-config.json
+#! @bash-interactive@/bin/bash -e
+exec -a "$0" "/nix/store/00000000000000000000000000000000-claude-code/bin/.claude-wrapped" --plugin-dir /nix/store/00000000000000000000000000000000-claude-code-hm-plugin "$@"
diff --git a/tests/modules/programs/claude-code/expected-plugin-manifest.json b/tests/modules/programs/claude-code/expected-plugin-manifest.json
new file mode 100644
index 00000000..be7b9d11
--- /dev/null
+++ b/tests/modules/programs/claude-code/expected-plugin-manifest.json
@@ -0,0 +1,3 @@
+{
+  "name": "claude-code-home-manager"
+}
diff --git a/tests/modules/programs/claude-code/lsp.nix b/tests/modules/programs/claude-code/lsp.nix
index f225a40e..5b74d589 100644
--- a/tests/modules/programs/claude-code/lsp.nix
+++ b/tests/modules/programs/claude-code/lsp.nix
@@ -32,7 +32,14 @@
   };
 
   nmt.script = ''
-    normalizedWrapper=$(normalizeStorePaths home-path/bin/claude)
-    assertFileContent $normalizedWrapper ${./expected-lsp-wrapper}
+    wrapperPath="$TESTED/home-path/bin/claude"
+    normalizedWrapper=$(normalizeStorePaths "$wrapperPath")
+    assertFileContent "$normalizedWrapper" ${./expected-lsp-wrapper}
+
+    pluginDir=$(grep -o -- '--plugin-dir /nix/store/[^ ]*' "$wrapperPath")
+    pluginDir="''${pluginDir#--plugin-dir }"
+    assertFileContent "$pluginDir/.claude-plugin/plugin.json" ${./expected-plugin-manifest.json}
+    assertFileContent "$pluginDir/.lsp.json" ${./expected-lsp-plugin.json}
+    assertPathNotExists "$pluginDir/.mcp.json"
   '';
 }
diff --git a/tests/modules/programs/claude-code/mcp-integration.nix b/tests/modules/programs/claude-code/mcp-integration.nix
index 9e9c0c66..66bf65ef 100644
--- a/tests/modules/programs/claude-code/mcp-integration.nix
+++ b/tests/modules/programs/claude-code/mcp-integration.nix
@@ -13,7 +13,7 @@
       };
       enable = true;
 
-      enableMcpIntagretion = true;
+      enableMcpIntegration = true;
 
       mcpServers = {
         github = {
@@ -66,7 +66,17 @@
   };
 
   nmt.script = ''
-    normalizedWrapper=$(normalizeStorePaths home-path/bin/claude)
-    assertFileContent $normalizedWrapper ${./expected-mcp-wrapper}
+    wrapperPath="$TESTED/home-path/bin/claude"
+    normalizedWrapper=$(normalizeStorePaths "$wrapperPath")
+    assertFileContent "$normalizedWrapper" ${./expected-mcp-wrapper}
+
+    pluginDir=$(grep -o -- '--plugin-dir /nix/store/[^ ]*' "$wrapperPath")
+    pluginDir="''${pluginDir#--plugin-dir }"
+    assertFileContent "$pluginDir/.claude-plugin/plugin.json" ${./expected-plugin-manifest.json}
+    assertFileRegex "$pluginDir/.mcp.json" '"github"'
+    assertFileRegex "$pluginDir/.mcp.json" '"database"'
+    assertFileRegex "$pluginDir/.mcp.json" '"/tmp"'
+    (! grep -q -- '/other-tmp' "$pluginDir/.mcp.json")
+    assertPathNotExists "$pluginDir/.lsp.json"
   '';
 }
diff --git a/tests/modules/programs/claude-code/mcp-lsp.nix b/tests/modules/programs/claude-code/mcp-lsp.nix
new file mode 100644
index 00000000..da45acca
--- /dev/null
+++ b/tests/modules/programs/claude-code/mcp-lsp.nix
@@ -0,0 +1,81 @@
+{ config, ... }:
+
+{
+  programs.claude-code = {
+    package = config.lib.test.mkStubPackage {
+      name = "claude-code";
+      buildScript = ''
+        mkdir -p $out/bin
+        touch $out/bin/claude
+        chmod 755 $out/bin/claude
+      '';
+    };
+    enable = true;
+
+    lspServers = {
+      go = {
+        command = "gopls";
+        args = [ "serve" ];
+        extensionToLanguage = {
+          ".go" = "go";
+        };
+      };
+      typescript = {
+        command = "typescript-language-server";
+        args = [ "--stdio" ];
+        extensionToLanguage = {
+          ".ts" = "typescript";
+          ".tsx" = "typescriptreact";
+        };
+      };
+    };
+
+    mcpServers = {
+      github = {
+        type = "http";
+        url = "https://api.githubcopilot.com/mcp/";
+      };
+      filesystem = {
+        type = "stdio";
+        command = "npx";
+        args = [
+          "-y"
+          "@modelcontextprotocol/server-filesystem"
+          "/tmp"
+        ];
+      };
+      database = {
+        type = "stdio";
+        command = "npx";
+        args = [
+          "-y"
+          "@bytebase/dbhub"
+          "--dsn"
+          "postgresql://user:pass@localhost:5432/db"
+        ];
+        env = {
+          DATABASE_URL = "postgresql://user:pass@localhost:5432/db";
+        };
+      };
+      customTransport = {
+        type = "websocket";
+        url = "wss://example.com/mcp";
+        customOption = "value";
+        timeout = 5000;
+      };
+    };
+  };
+
+  nmt.script = ''
+    wrapperPath="$TESTED/home-path/bin/claude"
+    normalizedWrapper=$(normalizeStorePaths "$wrapperPath")
+    assertFileContent "$normalizedWrapper" ${./expected-mcp-wrapper}
+
+    test "$(grep -o -- '--plugin-dir ' "$wrapperPath" | wc -l)" -eq 1
+    pluginDir=$(grep -o -- '--plugin-dir /nix/store/[^ ]*' "$wrapperPath")
+    pluginDir="''${pluginDir#--plugin-dir }"
+    assertFileContent "$pluginDir/.claude-plugin/plugin.json" ${./expected-plugin-manifest.json}
+    assertFileContent "$pluginDir/.mcp.json" ${./expected-mcp-plugin.json}
+    assertFileContent "$pluginDir/.lsp.json" ${./expected-lsp-plugin.json}
+  '';
+}
diff --git a/tests/modules/programs/claude-code/mcp.nix b/tests/modules/programs/claude-code/mcp.nix
index c95103c8..a923e4f2 100644
--- a/tests/modules/programs/claude-code/mcp.nix
+++ b/tests/modules/programs/claude-code/mcp.nix
@@ -49,7 +49,14 @@
   };
 
   nmt.script = ''
-    normalizedWrapper=$(normalizeStorePaths home-path/bin/claude)
-    assertFileContent $normalizedWrapper ${./expected-mcp-wrapper}
+    wrapperPath="$TESTED/home-path/bin/claude"
+    normalizedWrapper=$(normalizeStorePaths "$wrapperPath")
+    assertFileContent "$normalizedWrapper" ${./expected-mcp-wrapper}
+
+    pluginDir=$(grep -o -- '--plugin-dir /nix/store/[^ ]*' "$wrapperPath")
+    pluginDir="''${pluginDir#--plugin-dir }"
+    assertFileContent "$pluginDir/.claude-plugin/plugin.json" ${./expected-plugin-manifest.json}
+    assertFileContent "$pluginDir/.mcp.json" ${./expected-mcp-plugin.json}
+    assertPathNotExists "$pluginDir/.lsp.json"
   '';
 }