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

vitest.config.ts

@@ -0,0 +1,203 @@
+import { defineConfig } from 'vitest/config'
+
+export default defineConfig({
+  test: {
+    // Default configuration
+    globals: true,
+    setupFiles: ['./tests/test-setup.ts', './tests/setup.ts'],
+    testTimeout: 120000, // 120 seconds for TensorFlow operations
+    hookTimeout: 120000,
+    // Run tests in parallel with limited pool
+    pool: 'forks',
+    poolOptions: {
+      forks: {
+        singleFork: true, // Run all tests in a single fork to reduce memory usage
+        isolate: false, // Don't isolate tests to reduce overhead
+      }
+    },
+    // Limit concurrent tests to reduce memory usage
+    maxConcurrency: 1,
+    // Clear mocks between tests
+    clearMocks: true,
+    restoreMocks: true,
+    // Include test files
+    include: ['tests/**/*.{test,spec}.{js,ts}'],
+    // Default environment
+    environment: 'node',
+    // Exclude old test files
+    exclude: [
+      'node_modules/**',
+      'dist/**',
+      'scripts/**',
+      'examples/**',
+      '*.js' // Exclude old JS test files in root
+    ],
+    // Add environment options to help with TextEncoder issues
+    environmentOptions: {
+      env: {
+        FORCE_PATCHED_PLATFORM: 'true'
+      }
+    },
+    // Configure reporters for different output formats
+    reporters: [
+      // Default reporter for basic progress during test run
+      [
+        'default',
+        {
+          summary: true,
+          reportSummary: true,
+          // Show test titles for all tests
+          successfulTestOnly: false,
+          // Show a compact output
+          outputFile: false
+        }
+      ],
+      // JSON reporter for machine-readable output (can be used for CI/CD)
+      [
+        'json',
+        {
+          outputFile: './tests/results/test-results.json'
+        }
+      ]
+    ],
+    // Configure output for better visibility
+    silent: false,
+    // Configure error display for better readability
+    bail: 0,
+    // Disable coverage reports by default to reduce noise
+    coverage: {
+      enabled: false
+    },
+    // Don't show test statistics to reduce noise
+    logHeapUsage: false,
+    // Hide skipped tests to reduce noise
+    hideSkippedTests: true,
+    // Only show stack traces for failed tests
+    printConsoleTrace: false,
+    // Show test timing information in the summary
+    // showTimer: true,
+    // Aggressively filter out console output to only show test progress
+    onConsoleLog: (log: string, type: 'stdout' | 'stderr'): false | void => {
+      // For stdout, only allow critical error messages and test progress indicators
+      if (type === 'stdout') {
+        // Only allow through explicit test-related messages and critical errors
+        const allowedPatterns = [
+          'Error:',
+          'FAIL',
+          'PASS',
+          'WARNING:',
+          'test result',
+          'Test Files',
+          'Tests',
+          'Start at',
+          'Duration',
+          '✓',
+          '✗',
+          'running',
+          'suite'
+        ]
+
+        // If the log doesn't contain any allowed pattern, filter it out
+        if (!allowedPatterns.some((pattern) => log.includes(pattern))) {
+          return false
+        }
+      }
+
+      // For stderr, only show actual errors
+      if (
+        type === 'stderr' &&
+        !log.includes('Error:') &&
+        !log.includes('FAIL')
+      ) {
+        return false
+      }
+
+      // Expanded list of noise patterns to filter out
+      const noisePatterns: string[] = [
+        // Original patterns
+        'Brainy:',
+        'TensorFlow',
+        'Universal Sentence Encoder',
+        'Using file system storage',
+        'Using WebGL backend',
+        'Platform node',
+        'The kernel',
+        'for backend',
+        'is already registered',
+        'Hi there 👋',
+        'backend registration',
+        'webgl',
+        'cpu',
+        'Could not get context',
+        'Retrying',
+        'Skipping noun',
+        'due to dimension mismatch',
+        'Successfully loaded',
+        'model loaded',
+        'module structure',
+        'No default export',
+        'Using sentenceEncoderModule',
+        'Loading',
+        'Applying',
+        'Overwriting',
+        'Applied',
+        'running in Node.js environment',
+        'Pre-loading',
+        'has already been set',
+        // Additional patterns to filter out common console.log statements from tests
+        'Attempting to add',
+        'Successfully added',
+        'Test API server running',
+        'Text content not found',
+        'Searching for text',
+        'Expected ID:',
+        'Search returned',
+        'First result ID:',
+        'All result IDs:',
+        'Could not find result',
+        'Found result with matching ID:',
+        'console.log',
+        'console.info',
+        'console.debug'
+      ]
+
+      // Return false (don't show) if log contains any noise pattern
+      if (noisePatterns.some((pattern) => log.includes(pattern))) {
+        return false
+      }
+
+      // Additional filtering for common debug output patterns
+      if (
+        log.includes('Searching') ||
+        log.includes('Found') ||
+        log.includes('Created') ||
+        log.includes('Loaded') ||
+        log.includes('Processing') ||
+        log.includes('Initializing') ||
+        log.includes('Starting') ||
+        log.includes('Completed') ||
+        log.includes('Finished')
+      ) {
+        return false
+      }
+
+      return undefined // Show the log if it passes all filters
+    }
+
+    // Add a custom reporter configuration for a cleaner output
+    // outputDiffLines: 5, // Limit diff output lines for cleaner error reports
+    // outputFileMaxLines: 40, // Limit file output lines for cleaner error reports
+    // outputTruncateLength: 80 // Truncate long output lines
+  },
+  // Resolve configuration for proper module handling
+  resolve: {
+    alias: {
+      '@': './src',
+      '@tests': './tests'
+    }
+  },
+  // Define different configurations for different environments
+  define: {
+    'process.env.NODE_ENV': '"test"'
+  }
+})