fix: display only enabled tools in startup table (#171) (#176)

* fix: display only enabled tools in startup table (#171)

This commit fixes issue #171 and consolidates tool management into a
single registry, eliminating code duplication.

## Changes

1. **Fixed Issue #171**: Startup table now correctly shows only enabled tools
   - Renamed ToolRegistry.getToolsForSource() → getEnabledToolConfigs()
   - Updated getToolsForSource() in tool-metadata.ts to respect registry

2. **Unified tool handling**: Eliminated separate code paths for built-in vs custom tools
   - Refactored getToolsForSource() to use uniform iteration pattern
   - Single loop processes all tool types consistently

3. **Consolidated validation**: Removed CustomToolRegistry entirely
   - Moved all validation logic into ToolRegistry
   - Deleted custom-tool-registry.ts (220 lines)
   - Simplified server initialization

## Impact

- Net reduction: 77 lines removed
- Single source of truth for all tool management
- All 357 unit tests pass
- Backward compatible

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

* fix: initialize ToolRegistry in sources.integration.test.ts

The sources API integration test was failing because it didn't initialize
the ToolRegistry before making API calls. The test now properly initializes
the registry with the fixture config in beforeAll.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

---------

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

Author: tianzhou

src/api/__tests__/sources.integration.test.ts

@@ -1,10 +1,11 @@
 import { describe, it, expect, beforeAll, afterAll } from 'vitest';
 import express, { Application } from 'express';
-import { setupManagerWithFixture, FIXTURES } from '../../__fixtures__/helpers.js';
+import { setupManagerWithFixture, FIXTURES, loadFixtureConfig } from '../../__fixtures__/helpers.js';
 import type { ConnectorManager } from '../../connectors/manager.js';
 import { listSources, getSource } from '../sources.js';
 import type { components } from '../openapi.js';
 import { Server } from 'http';
+import { initializeToolRegistry } from '../../tools/registry.js';
 
 // Import SQLite connector to ensure it's registered
 import '../../connectors/sqlite/index.js';
@@ -27,6 +28,10 @@ describe('Data Sources API Integration Tests', () => {
     // - writable_unlimited: readonly=false, no max_rows
     manager = await setupManagerWithFixture(FIXTURES.READONLY_MAXROWS);
 
+    // Initialize ToolRegistry with fixture config
+    const sources = loadFixtureConfig(FIXTURES.READONLY_MAXROWS);
+    initializeToolRegistry({ sources, tools: [] });
+
     // Set up Express app with API routes
     app = express();
     app.use(express.json());

src/server.ts

@@ -107,25 +107,6 @@ See documentation for more details on configuring database connections.
     });
     console.error("Tool registry initialized");
 
-    // Initialize custom tool registry early (needed for API routes)
-    // Only initialize once (idempotent - safe for multiple MCP client connections)
-    if (sourceConfigsData.tools && sourceConfigsData.tools.length > 0) {
-      const { customToolRegistry } = await import("./tools/custom-tool-registry.js");
-      const { BUILTIN_TOOLS } = await import("./tools/builtin-tools.js");
-
-      if (!customToolRegistry.isInitialized()) {
-        // Filter out built-in tools - custom tool registry only handles custom tools
-        const customTools = sourceConfigsData.tools.filter(
-          (tool) => !(BUILTIN_TOOLS as readonly string[]).includes(tool.name)
-        );
-
-        if (customTools.length > 0) {
-          customToolRegistry.initialize(customTools);
-          console.error(`Custom tool registry initialized with ${customTools.length} tool(s)`);
-        }
-      }
-    }
-
     // Create MCP server factory function for HTTP transport
     // Note: This must be created AFTER ConnectorManager is initialized
     const createServer = () => {
@@ -135,7 +116,7 @@ See documentation for more details on configuring database connections.
       });
 
       // Register tools (both built-in and custom)
-      // Custom tools are already initialized in customToolRegistry by the code above
+      // All tools are validated and managed by the ToolRegistry
       registerTools(server);
 
       return server;

src/tools/custom-tool-registry.ts

@@ -25,7 +25,7 @@ export function registerTools(server: McpServer): void {
 
   // Register all enabled tools (both built-in and custom) for each source
   for (const sourceId of sourceIds) {
-    const enabledTools = registry.getToolsForSource(sourceId);
+    const enabledTools = registry.getEnabledToolConfigs(sourceId);
     const sourceConfig = ConnectorManager.getSourceConfig(sourceId)!;
     const dbType = sourceConfig.type;
     const isDefault = sourceIds[0] === sourceId;