Fix Claude Code MCP server configuration approach

Replace incorrect mcp.json configuration with proper CLI-based setup using activation scripts. This ensures MCP servers are configured as user-scoped (global) and safely preserves Claude's existing configuration data.

Author: svnlto

common/claude-code/default.nix

@@ -18,7 +18,6 @@
   # Create and manage ~/.claude directory
   home.file.".claude/settings.json".source = ./settings.json;
   home.file.".claude/CLAUDE.md".source = ./CLAUDE.md;
-  home.file.".claude/.mcp.json".source = ./mcp.json;
 
 
   # Combine local commands with linear commands
@@ -54,4 +53,21 @@
     fi
   '';
 
+  # Setup MCP servers after Claude Code is installed
+  home.activation.setupMcpServers = lib.hm.dag.entryAfter ["installClaudeCode"] ''
+    PATH="${pkgs.nodejs_22}/bin:$PATH"
+    export NPM_CONFIG_PREFIX="$HOME/.npm-global"
+    
+    # Only add if not already configured
+    if ! claude mcp list | grep -q "context7"; then
+      echo "Configuring MCP servers..."
+      claude mcp add --scope user context7 npx -y @context-labs/context7-server
+      claude mcp add --scope user code-reasoning npx -y @mettamatt/code-reasoning  
+      claude mcp add --scope user sequential-thinking npx -y @modelcontextprotocol/server-sequential-thinking
+      echo "MCP servers configured successfully"
+    else
+      echo "MCP servers already configured"
+    fi
+  '';
+
 }