fix: Resolve soft delete and add encrypted config support

- Fix soft delete functionality by filtering out deleted items in search results
- Add support for encrypted configuration storage and retrieval
- Copy test suite and vitest config to ensure all functionality works
- Maintain all core brainy functionality during repository cleanup

tests/setup.ts

@@ -0,0 +1,90 @@
+/**
+ * Simple test setup for Brainy library
+ * No direct TensorFlow references - patches are handled internally by Brainy
+ */
+
+import { beforeEach, afterEach, afterAll } from 'vitest'
+import { existsSync, rmSync } from 'fs'
+import { join } from 'path'
+
+// Define the test utilities type for reuse
+type TestUtilsType = {
+  createTestVector: (dimensions: number) => number[]
+  timeout: number
+}
+
+// Extend global type definitions for both global and globalThis
+declare global {
+  let testUtils: TestUtilsType | undefined
+  let __ENV__: any
+}
+
+// Explicitly declare globalThis interface to ensure TypeScript recognizes these properties
+declare global {
+  interface globalThis {
+    testUtils?: TestUtilsType | undefined
+    __ENV__?: any
+  }
+}
+
+// Clean up between tests
+beforeEach(() => {
+  // Clear any global state that might interfere with tests
+  if (typeof globalThis !== 'undefined' && globalThis.__ENV__) {
+    delete globalThis.__ENV__
+  }
+  if (typeof global !== 'undefined' && global.__ENV__) {
+    delete global.__ENV__
+  }
+  
+  // Clean up test data directory to prevent file accumulation
+  const testDataDir = join(process.cwd(), 'brainy-data')
+  if (existsSync(testDataDir)) {
+    try {
+      rmSync(testDataDir, { recursive: true, force: true })
+    } catch (error) {
+      // Ignore errors during cleanup
+    }
+  }
+})
+
+// Clean up after each test
+afterEach(() => {
+  // Force garbage collection if available (requires --expose-gc flag)
+  if (global.gc) {
+    global.gc()
+  }
+})
+
+// Final cleanup after all tests
+afterAll(() => {
+  // Clean up test data directory
+  const testDataDir = join(process.cwd(), 'brainy-data')
+  if (existsSync(testDataDir)) {
+    try {
+      rmSync(testDataDir, { recursive: true, force: true })
+    } catch (error) {
+      // Ignore errors during cleanup
+    }
+  }
+})
+
+// Add simple test utilities to both global and globalThis for compatibility
+const testUtilsObject = {
+  // Create a simple test vector with predictable values
+  createTestVector: (dimensions: number): number[] => {
+    return Array.from({ length: dimensions }, (_, i) => (i + 1) / dimensions)
+  },
+
+  // Standard timeout for async operations
+  timeout: 30000
+}
+
+global.testUtils = testUtilsObject
+globalThis.testUtils = testUtilsObject
+
+// Set a clear test environment flag for embedding system
+globalThis.__BRAINY_TEST_ENV__ = true
+if (typeof global !== 'undefined') {
+  (global as any).__BRAINY_TEST_ENV__ = true
+}