feat: brain.find() excludes VFS by default (Option 3C)

Added includeVFS parameter to FindParams:
- brain.find() excludes VFS entities by default (clean knowledge graph)
- Opt-in with brain.find({ includeVFS: true })
- Automatically excludes VFS in all query paths (empty, metadata, vector)
- Respects explicit where: { isVFS: ... } queries

Implementation:
- Empty query path: Apply VFS filtering even with no criteria
- Metadata query path: Filter out isVFS: true by default
- Vector search path: Apply VFS filter after search
- Skip auto-exclusion if where clause explicitly queries isVFS

Architecture (Option 3C):
- VFS entities are first-class graph entities
- Marked with isVFS: true flag
- Separated via filtering, not storage
- Enables VFS-knowledge relationships

Moved internal docs to .strategy/:
- README_STORAGE_EXPLORATION.md
- EXPLORATION_SUMMARY.md
- STORAGE_FILES_REFERENCE.md
- STORAGE_ADAPTER_QUICK_REFERENCE.md
- SECURITY.md

tests/manual/vfs-isvfs-diagnostic.test.ts

@@ -0,0 +1,90 @@
+/**
+ * Diagnostic: Check if isVFS flag is actually being stored
+ */
+
+import { describe, it, expect, beforeAll, afterAll } from 'vitest'
+import { Brainy } from '../../src/brainy.js'
+import { NounType } from '../../src/types/graphTypes.js'
+import * as fs from 'fs'
+import * as path from 'path'
+
+describe('isVFS Flag Diagnostic', () => {
+  const testDir = path.join(process.cwd(), 'test-isvfs-diagnostic')
+  let brain: Brainy
+
+  beforeAll(async () => {
+    if (fs.existsSync(testDir)) {
+      fs.rmSync(testDir, { recursive: true, force: true })
+    }
+    fs.mkdirSync(testDir, { recursive: true })
+
+    brain = new Brainy({
+      storage: {
+        type: 'filesystem',
+        options: { path: testDir }
+      }
+    })
+    await brain.init()
+  })
+
+  afterAll(() => {
+    if (fs.existsSync(testDir)) {
+      fs.rmSync(testDir, { recursive: true, force: true })
+    }
+  })
+
+  it('should show what entities are created', async () => {
+    // Create VFS file
+    const vfs = brain.vfs()
+    await vfs.init()
+    await vfs.writeFile('/test.txt', 'Hello World')
+
+    // Get ALL entities
+    console.log('\n📋 All entities in database:')
+    const allEntities = await brain.find({ limit: 100, includeVFS: true })
+    console.log(`   Total: ${allEntities.length}`)
+
+    for (const entity of allEntities) {
+      console.log(`\n   Entity: ${entity.id}`)
+      console.log(`      Type: ${entity.type}`)
+      console.log(`      Metadata keys: ${Object.keys(entity.metadata || {}).join(', ')}`)
+      if (entity.metadata?.path) {
+        console.log(`      Path: ${entity.metadata.path}`)
+      }
+      if (entity.metadata?.vfsType) {
+        console.log(`      VfsType: ${entity.metadata.vfsType}`)
+      }
+      if (entity.metadata?.isVFS !== undefined) {
+        console.log(`      isVFS: ${entity.metadata.isVFS}`)
+      }
+      if (entity.metadata?.name) {
+        console.log(`      Name: ${entity.metadata.name}`)
+      }
+    }
+
+    // Try different queries
+    console.log('\n\n📋 Query 1: brain.find({ limit: 100 }) [default, no includeVFS]')
+    const query1 = await brain.find({ limit: 100 })
+    console.log(`   Results: ${query1.length}`)
+
+    console.log('\n📋 Query 2: brain.find({ limit: 100, includeVFS: true })')
+    const query2 = await brain.find({ limit: 100, includeVFS: true })
+    console.log(`   Results: ${query2.length}`)
+
+    console.log('\n📋 Query 3: brain.find({ where: { isVFS: true } })')
+    const query3 = await brain.find({ where: { isVFS: true }, limit: 100 })
+    console.log(`   Results: ${query3.length}`)
+
+    console.log('\n📋 Query 4: brain.find({ where: { path: "/test.txt" } })')
+    const query4 = await brain.find({ where: { path: '/test.txt' }, limit: 100 })
+    console.log(`   Results: ${query4.length}`)
+
+    console.log('\n📋 Query 5: brain.find({ type: NounType.Document })')
+    const query5 = await brain.find({ type: NounType.Document, limit: 100 })
+    console.log(`   Results: ${query5.length}`)
+
+    console.log('\n📋 Query 6: brain.find({ type: NounType.Document, includeVFS: true })')
+    const query6 = await brain.find({ type: NounType.Document, includeVFS: true, limit: 100 })
+    console.log(`   Results: ${query6.length}`)
+  })
+})