Add tests for server factory, registrations, and resources

Additional test coverage:
- server/index.ts: createServer factory, cleanup function (91% coverage)
- tools/index.ts: registerTools, registerConditionalTools (100% coverage)
- prompts/index.ts: registerPrompts (100% coverage)
- resources/index.ts: registerResources, readInstructions (88% coverage)
- resources/files.ts: registerFileResources (54% coverage)
- resources/subscriptions.ts: handlers, begin/stop updates (47% coverage)

Test count: 124 tests (was 102)
Coverage: 71.35% overall (was 64.73%)
- Tools: 93.12%
- Prompts: 90.53%
- Server: 62.93%
- Resources: 65.44%

Note: Transport files (stdio.ts, sse.ts, streamableHttp.ts) are entry
points that start Express servers. These require integration tests
rather than unit tests.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/everything/__tests__/registrations.test.ts

@@ -0,0 +1,134 @@
+import { describe, it, expect, vi } from 'vitest';
+import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+
+// Create mock server
+function createMockServer() {
+  return {
+    registerTool: vi.fn(),
+    registerPrompt: vi.fn(),
+    registerResource: vi.fn(),
+    server: {
+      getClientCapabilities: vi.fn(() => ({})),
+      setRequestHandler: vi.fn(),
+    },
+    sendLoggingMessage: vi.fn(),
+    sendResourceUpdated: vi.fn(),
+  } as unknown as McpServer;
+}
+
+describe('Registration Index Files', () => {
+  describe('tools/index.ts', () => {
+    it('should register all standard tools', async () => {
+      const { registerTools } = await import('../tools/index.js');
+      const mockServer = createMockServer();
+
+      registerTools(mockServer);
+
+      // Should register 12 standard tools (non-conditional)
+      expect(mockServer.registerTool).toHaveBeenCalledTimes(12);
+
+      // Verify specific tools are registered
+      const registeredTools = (mockServer.registerTool as any).mock.calls.map(
+        (call: any[]) => call[0]
+      );
+      expect(registeredTools).toContain('echo');
+      expect(registeredTools).toContain('get-sum');
+      expect(registeredTools).toContain('get-env');
+      expect(registeredTools).toContain('get-tiny-image');
+      expect(registeredTools).toContain('get-structured-content');
+      expect(registeredTools).toContain('get-annotated-message');
+      expect(registeredTools).toContain('trigger-long-running-operation');
+      expect(registeredTools).toContain('get-resource-links');
+      expect(registeredTools).toContain('get-resource-reference');
+      expect(registeredTools).toContain('gzip-file-as-resource');
+      expect(registeredTools).toContain('toggle-simulated-logging');
+      expect(registeredTools).toContain('toggle-subscriber-updates');
+    });
+
+    it('should register conditional tools based on capabilities', async () => {
+      const { registerConditionalTools } = await import('../tools/index.js');
+
+      // Server with all capabilities
+      const mockServerWithCapabilities = {
+        registerTool: vi.fn(),
+        server: {
+          getClientCapabilities: vi.fn(() => ({
+            roots: {},
+            elicitation: {},
+            sampling: {},
+          })),
+        },
+      } as unknown as McpServer;
+
+      registerConditionalTools(mockServerWithCapabilities);
+
+      // Should register 3 conditional tools when all capabilities present
+      expect(mockServerWithCapabilities.registerTool).toHaveBeenCalledTimes(3);
+
+      const registeredTools = (
+        mockServerWithCapabilities.registerTool as any
+      ).mock.calls.map((call: any[]) => call[0]);
+      expect(registeredTools).toContain('get-roots-list');
+      expect(registeredTools).toContain('trigger-elicitation-request');
+      expect(registeredTools).toContain('trigger-sampling-request');
+    });
+
+    it('should not register conditional tools when capabilities missing', async () => {
+      const { registerConditionalTools } = await import('../tools/index.js');
+
+      const mockServerNoCapabilities = {
+        registerTool: vi.fn(),
+        server: {
+          getClientCapabilities: vi.fn(() => ({})),
+        },
+      } as unknown as McpServer;
+
+      registerConditionalTools(mockServerNoCapabilities);
+
+      // Should not register any tools when capabilities are missing
+      expect(mockServerNoCapabilities.registerTool).not.toHaveBeenCalled();
+    });
+  });
+
+  describe('prompts/index.ts', () => {
+    it('should register all prompts', async () => {
+      const { registerPrompts } = await import('../prompts/index.js');
+      const mockServer = createMockServer();
+
+      registerPrompts(mockServer);
+
+      // Should register 4 prompts
+      expect(mockServer.registerPrompt).toHaveBeenCalledTimes(4);
+
+      const registeredPrompts = (mockServer.registerPrompt as any).mock.calls.map(
+        (call: any[]) => call[0]
+      );
+      expect(registeredPrompts).toContain('simple-prompt');
+      expect(registeredPrompts).toContain('args-prompt');
+      expect(registeredPrompts).toContain('completable-prompt');
+      expect(registeredPrompts).toContain('resource-prompt');
+    });
+  });
+
+  describe('resources/index.ts', () => {
+    it('should register resource templates', async () => {
+      const { registerResources } = await import('../resources/index.js');
+      const mockServer = createMockServer();
+
+      registerResources(mockServer);
+
+      // Should register at least the 2 resource templates (text and blob)
+      expect(mockServer.registerResource).toHaveBeenCalled();
+    });
+
+    it('should read instructions from file', async () => {
+      const { readInstructions } = await import('../resources/index.js');
+
+      const instructions = readInstructions();
+
+      // Should return a string (either content or error message)
+      expect(typeof instructions).toBe('string');
+      expect(instructions.length).toBeGreaterThan(0);
+    });
+  });
+});