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/database-operations.test.ts

@@ -0,0 +1,64 @@
+import { describe, it, expect } from 'vitest'
+import { BrainyData } from '../dist/unified.js'
+
+describe('Database Operations', () => {
+  let db: BrainyData
+  
+  beforeEach(async () => {
+    db = new BrainyData()
+    await db.init()
+  })
+  
+  it('should initialize and return database status', async () => {
+    const status = await db.status()
+    expect(status).toBeDefined()
+    // The structure of status might vary, just check it exists
+  })
+  
+  it('should return statistics', async () => {
+    const stats = await db.getStatistics()
+    expect(stats).toBeDefined()
+    // The structure of stats might vary, just check it exists
+  })
+  
+  it('should retrieve all nouns', async () => {
+    const nouns = await db.getAllNouns()
+    expect(Array.isArray(nouns)).toBe(true)
+  })
+  
+  it('should retrieve all verbs', async () => {
+    const verbs = await db.getAllVerbs()
+    expect(Array.isArray(verbs)).toBe(true)
+  })
+  
+  it('should perform a search operation', async () => {
+    const searchResults = await db.searchText('test', 10)
+    expect(Array.isArray(searchResults)).toBe(true)
+  })
+  
+  it('should add and retrieve an item', async () => {
+    // Add a test item
+    const testText = 'This is a test item for searching'
+    const metadata = { noun: 'Thing', category: 'test' }
+    const id = await db.add(testText, metadata)
+    
+    // Verify the item was added
+    expect(id).toBeDefined()
+    
+    // Retrieve the item
+    const noun = await db.get(id)
+    expect(noun).toBeDefined()
+    expect(noun.id).toBe(id)
+    
+    // Check that the metadata contains our properties
+    // (The system might add additional properties)
+    expect(noun.metadata.category).toBe('test')
+    
+    // Search for the item
+    const searchResults = await db.searchText('test', 10)
+    expect(searchResults.length).toBeGreaterThan(0)
+    
+    // Clean up
+    await db.delete(id)
+  })
+})