1 files changed, 47 insertions, 12 deletions

diff --git a/src/main/claude/index.ts b/src/main/claude/index.ts
index ca54164..8cf512c 100644
--- a/src/main/claude/index.ts
+++ b/src/main/claude/index.ts
@@ -53,7 +53,38 @@ export async function sendMessage({
 
   // Load MCP servers config (JSON string → object, or undefined if not set)
   const mcpServersJson = getSetting("mcpServers");
-  const mcpServers = mcpServersJson ? JSON.parse(mcpServersJson) : undefined;
+  const mcpServersConfig = mcpServersJson ? JSON.parse(mcpServersJson) : undefined;
+
+  // Build allowedTools list from enabled MCP tools
+  // Format: mcp__servername__toolname
+  const mcpAllowedTools: string[] = [];
+  if (mcpServersConfig) {
+    for (const [serverName, config] of Object.entries(mcpServersConfig)) {
+      const serverConfig = config as {
+        enabledTools?: string[];
+        discoveredTools?: Array<{ name: string }>;
+      };
+      // Use enabledTools if available, otherwise allow all discovered tools
+      const enabledTools = serverConfig.enabledTools ||
+        serverConfig.discoveredTools?.map((t) => t.name) ||
+        [];
+      for (const toolName of enabledTools) {
+        mcpAllowedTools.push(`mcp__${serverName}__${toolName}`);
+      }
+    }
+  }
+
+  // Strip tool management fields from config before passing to SDK
+  // SDK only needs: type, command, args, env, url, headers
+  let mcpServers: Record<string, unknown> | undefined;
+  if (mcpServersConfig && Object.keys(mcpServersConfig).length > 0) {
+    mcpServers = Object.fromEntries(
+      Object.entries(mcpServersConfig).map(([name, config]) => {
+        const { discoveredTools, enabledTools, ...sdkConfig } = config as Record<string, unknown>;
+        return [name, sdkConfig];
+      })
+    );
+  }
 
   const phaseConfig = getPhaseConfig(
     session.phase as Phase,
@@ -62,28 +93,32 @@ export async function sendMessage({
     customSystemPrompt
   );
 
+  // Build allowedTools for this phase
+  const allowedTools: string[] = [];
+  if (session.phase === "implement") {
+    // Allow git inspection in implement phase
+    allowedTools.push("Bash(git status*)", "Bash(git log*)", "Bash(git diff*)");
+  }
+  if (mcpAllowedTools.length > 0) {
+    // Add enabled MCP tools
+    allowedTools.push(...mcpAllowedTools);
+  }
+
   const q = query({
     prompt: message,
     options: {
       cwd: project.path,
       model: configuredModel,
-      mcpServers,
+      // eslint-disable-next-line @typescript-eslint/no-explicit-any
+      mcpServers: mcpServers as any,
       resume: session.claude_session_id ?? undefined,
       tools: phaseConfig.tools,
       permissionMode: phaseConfig.permissionMode,
       // Required companion flag when bypassPermissions is active
       allowDangerouslySkipPermissions: phaseConfig.permissionMode === "bypassPermissions",
       systemPrompt: phaseConfig.systemPrompt,
-      // Allow Claude to inspect git state during implementation without prompts.
-      // git add/commit intentionally omitted — the app handles those.
-      ...(session.phase === "implement" && {
-        allowedTools: ["Bash(git status*)", "Bash(git log*)", "Bash(git diff*)"],
-      }),
-      // When MCPs are configured in research phase, bypass permissions to allow MCP tools
-      ...(session.phase === "research" && mcpServers && {
-        permissionMode: "bypassPermissions" as const,
-        allowDangerouslySkipPermissions: true,
-      }),
+      // Pre-approve specific tools to avoid permission prompts
+      ...(allowedTools.length > 0 && { allowedTools }),
     },
   });