fix(doctor): detect MCP server in project-level settings (#1104)

Apply same fix as #1091 to isMCPServerInstalled(): check all three
settings locations (user-level, project-level, and project-local).

- Extract checkMCPInSettings() helper function
- Check ~/.claude/settings.json, .claude/settings.json, and
  .claude/settings.local.json
- Add TestIsMCPServerInstalledProjectLevel with positive and negative cases

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/doctor/claude.go

@@ -142,15 +142,39 @@ func checkPluginInSettings(settingsPath string) bool {
 	return false
 }
 
-// isMCPServerInstalled checks if MCP server is configured
+// isMCPServerInstalled checks if MCP server is configured.
+// It checks user-level (~/.claude/settings.json) and project-level settings
+// (.claude/settings.json and .claude/settings.local.json).
 func isMCPServerInstalled() bool {
 	home, err := os.UserHomeDir()
 	if err != nil {
 		return false
 	}
 
-	settingsPath := filepath.Join(home, ".claude/settings.json")
+	// Check user-level settings
-	data, err := os.ReadFile(settingsPath) // #nosec G304 -- settingsPath is constructed from user home dir, not user input
+	userSettings := filepath.Join(home, ".claude", "settings.json")
+	if checkMCPInSettings(userSettings) {
+		return true
+	}
+
+	// Check project-level settings
+	projectSettings := filepath.Join(".claude", "settings.json")
+	if checkMCPInSettings(projectSettings) {
+		return true
+	}
+
+	// Check project-level local settings (gitignored)
+	projectLocalSettings := filepath.Join(".claude", "settings.local.json")
+	if checkMCPInSettings(projectLocalSettings) {
+		return true
+	}
+
+	return false
+}
+
+// checkMCPInSettings checks if beads MCP server is configured in a settings file
+func checkMCPInSettings(settingsPath string) bool {
+	data, err := os.ReadFile(settingsPath) // #nosec G304 -- settingsPath is constructed from known safe locations, not user input
 	if err != nil {
 		return false
 	}

cmd/bd/doctor/claude_test.go

@@ -169,6 +169,64 @@ func TestIsMCPServerInstalled(t *testing.T) {
 	}
 }
 
+func TestIsMCPServerInstalledProjectLevel(t *testing.T) {
+	mcpContent := `{"mcpServers":{"beads":{"command":"beads-mcp"}}}`
+
+	// Test that MCP server is detected in each project-level settings file
+	for _, filename := range []string{"settings.json", "settings.local.json"} {
+		t.Run(filename, func(t *testing.T) {
+			tmpDir := t.TempDir()
+			t.Chdir(tmpDir)
+
+			if err := os.MkdirAll(".claude", 0o755); err != nil {
+				t.Fatal(err)
+			}
+			if err := os.WriteFile(filepath.Join(".claude", filename), []byte(mcpContent), 0o644); err != nil {
+				t.Fatal(err)
+			}
+
+			if !isMCPServerInstalled() {
+				t.Errorf("expected to detect MCP server in .claude/%s", filename)
+			}
+		})
+	}
+
+	// Test negative cases
+	t.Run("no mcpServers section", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		t.Chdir(tmpDir)
+
+		if err := os.MkdirAll(".claude", 0o755); err != nil {
+			t.Fatal(err)
+		}
+		content := `{"hooks":{}}`
+		if err := os.WriteFile(filepath.Join(".claude", "settings.json"), []byte(content), 0o644); err != nil {
+			t.Fatal(err)
+		}
+
+		if isMCPServerInstalled() {
+			t.Error("expected NOT to detect MCP server when mcpServers section missing")
+		}
+	})
+
+	t.Run("mcpServers but not beads", func(t *testing.T) {
+		tmpDir := t.TempDir()
+		t.Chdir(tmpDir)
+
+		if err := os.MkdirAll(".claude", 0o755); err != nil {
+			t.Fatal(err)
+		}
+		content := `{"mcpServers":{"other-server":{"command":"other"}}}`
+		if err := os.WriteFile(filepath.Join(".claude", "settings.json"), []byte(content), 0o644); err != nil {
+			t.Fatal(err)
+		}
+
+		if isMCPServerInstalled() {
+			t.Error("expected NOT to detect MCP server when beads not present")
+		}
+	})
+}
+
 func TestIsBeadsPluginInstalled(t *testing.T) {
 	// Similar sanity check for plugin detection
 	result := isBeadsPluginInstalled()