claude-code: reject disabled mcp servers instead of dropping

Filtering disabled shared servers out of `.mcp.json` (#9457) collapsed
"present but disabled" and "absent" into the same output, so a server
set
`enabled = false` for OpenCode could no longer remain present in Claude
Code. `.mcp.json` has no per-server `enabled` field, but settings.json
does via `disabledMcpjsonServers`.

Keep disabled servers in `.mcp.json` and list them under
`disabledMcpjsonServers` (merged with any user-set value). This honors
the
disabled intent without dropping the server, and covers both shared and
Claude Code-native servers.

modules/programs/claude-code.nix

@@ -38,10 +38,15 @@ let
       ];
     };
 
-  transformedMcpServers = lib.optionalAttrs (cfg.enableMcpIntegration && config.programs.mcp.enable) (
-    lib.mapAttrs transformMcpServer (
-      lib.filterAttrs (_: isMcpServerEnabled) config.programs.mcp.servers
-    )
+  # Shared MCP servers participate only when both integrations are enabled.
+  sharedMcpServers = lib.optionalAttrs (
+    cfg.enableMcpIntegration && config.programs.mcp.enable
+  ) config.programs.mcp.servers;
+
+  transformedMcpServers = lib.mapAttrs transformMcpServer sharedMcpServers;
+
+  disabledMcpServerNames = lib.attrNames (
+    lib.filterAttrs (_: server: !(isMcpServerEnabled server)) (sharedMcpServers // cfg.mcpServers)
   );
 
   mkContentOption =
@@ -111,6 +116,12 @@ in
         Note: Settings defined in {option}`programs.mcp.servers` are merged
         with {option}`programs.claude-code.mcpServers`, with Claude Code servers
         taking precedence.
+
+        Servers marked disabled (via `enabled = false` or `disabled = true`)
+        are still written to {file}`.mcp.json` but rejected through
+        `disabledMcpjsonServers` in {file}`settings.json`, since Claude Code
+        has no per-server `enabled` field. This keeps a disabled server
+        present (and re-enableable) instead of dropping it.
       '';
     };
 
@@ -701,7 +712,7 @@ in
         };
 
         file = lib.mkMerge [
-          (lib.mkIf (cfg.settings != { } || cfg.marketplaces != { }) {
+          (lib.mkIf (cfg.settings != { } || cfg.marketplaces != { } || disabledMcpServerNames != [ ]) {
             "${cfg.configDir}/settings.json".source = jsonFormat.generate "claude-code-settings.json" (
               cfg.settings
               // {
@@ -710,6 +721,11 @@ in
               // optionalAttrs (cfg.marketplaces != { }) {
                 extraKnownMarketplaces = lib.mapAttrs mkMarketplaceEntry cfg.marketplaces;
               }
+              // optionalAttrs (disabledMcpServerNames != [ ]) {
+                disabledMcpjsonServers = lib.unique (
+                  (cfg.settings.disabledMcpjsonServers or [ ]) ++ disabledMcpServerNames
+                );
+              }
             );
           })
           (

tests/modules/programs/claude-code/expected-mcp-integration-plugin.json

@@ -0,0 +1,43 @@
+{
+  "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"
+    },
+    "disabled-server": {
+      "args": [
+        "test"
+      ],
+      "command": "echo",
+      "type": "stdio"
+    },
+    "filesystem": {
+      "args": [
+        "-y",
+        "@modelcontextprotocol/server-filesystem",
+        "/tmp"
+      ],
+      "command": "npx",
+      "type": "stdio"
+    },
+    "github": {
+      "type": "http",
+      "url": "https://api.githubcopilot.com/mcp/"
+    }
+  }
+}

tests/modules/programs/claude-code/expected-mcp-settings.json

@@ -0,0 +1,6 @@
+{
+  "$schema": "https://json.schemastore.org/claude-code-settings.json",
+  "disabledMcpjsonServers": [
+    "disabled-server"
+  ]
+}

tests/modules/programs/claude-code/mcp-integration.nix

@@ -79,7 +79,10 @@
     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/.mcp.json" ${./expected-mcp-integration-plugin.json}
     assertPathNotExists "$pluginDir/.lsp.json"
+
+    settingsPath="$TESTED/home-files/.claude/settings.json"
+    assertFileContent "$settingsPath" ${./expected-mcp-settings.json}
   '';
 }