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__/server.test.ts

@@ -0,0 +1,62 @@
+import { describe, it, expect, vi } from 'vitest';
+import { createServer } from '../server/index.js';
+
+describe('Server Factory', () => {
+  describe('createServer', () => {
+    it('should return a ServerFactoryResponse object', () => {
+      const result = createServer();
+
+      expect(result).toHaveProperty('server');
+      expect(result).toHaveProperty('cleanup');
+    });
+
+    it('should return a cleanup function', () => {
+      const { cleanup } = createServer();
+
+      expect(typeof cleanup).toBe('function');
+    });
+
+    it('should create an McpServer instance', () => {
+      const { server } = createServer();
+
+      expect(server).toBeDefined();
+      expect(server.server).toBeDefined();
+    });
+
+    it('should have tools capability enabled', () => {
+      const { server } = createServer();
+
+      // Server should be properly configured
+      expect(server).toBeDefined();
+    });
+
+    it('should cleanup without throwing errors', () => {
+      const { cleanup } = createServer();
+
+      // Cleanup should not throw when called with a session ID
+      expect(() => cleanup('test-session')).not.toThrow();
+    });
+
+    it('should cleanup without throwing errors when sessionId is undefined', () => {
+      const { cleanup } = createServer();
+
+      // Cleanup should not throw when called without a session ID
+      expect(() => cleanup()).not.toThrow();
+    });
+
+    it('should allow multiple servers to be created', () => {
+      const result1 = createServer();
+      const result2 = createServer();
+
+      expect(result1.server).toBeDefined();
+      expect(result2.server).toBeDefined();
+      expect(result1.server).not.toBe(result2.server);
+    });
+
+    it('should have an oninitialized handler set', () => {
+      const { server } = createServer();
+
+      expect(server.server.oninitialized).toBeDefined();
+    });
+  });
+});