feat: add confidence/weight to Entity and flatten Result fields for convenient access

Add confidence and weight properties to Entity interface and flatten Result fields to top level for improved developer experience and API consistency.

Breaking Changes: None (all changes are backward compatible)

Phase 2 - Entity Confidence & Weight:
- Add confidence (type classification certainty) and weight (entity importance) to Entity interface
- Add confidence/weight parameters to AddParams and UpdateParams
- Update convertNounToEntity() to extract confidence/weight from storage
- Update add() and update() methods to preserve confidence/weight in metadata
- Enable developers to specify and access entity confidence/weight scores

Phase 3 - Result Field Flattening:
- Flatten commonly-used entity fields (type, metadata, data, confidence, weight) to Result top level
- Add createResult() helper for consistent Result construction
- Update all find() code paths to use createResult()
- Enable direct access: result.metadata instead of result.entity.metadata
- Preserve full entity in result.entity for backward compatibility

VFS Fix (from previous work):
- Fix VFSStructureGenerator to use brain.vfs() cached instance instead of creating separate instance
- Improve VFS error messages with step-by-step guidance
- Update examples to show correct vfs.init() usage
- Add comprehensive VFS import verification tests

Documentation Updates:
- Update API_REFERENCE.md with confidence/weight examples and flattened Result documentation
- Enhance JSDoc for add(), get(), find(), similar() with v4.3.0 examples
- Document Result structure changes and backward compatibility
- Add migration examples showing both old and new access patterns

Tests:
- Add 16 comprehensive tests for Entity confidence/weight exposure
- Add tests for Result field flattening
- Add tests for backward compatibility
- All tests passing (16/16)

API Consistency:
- Entity: direct access to confidence/weight
- Result: flattened fields + nested entity (both work)
- Relation: already had confidence/weight (consistent)
- VFS: inherits from Entity (automatic)

Files Changed:
- src/types/brainy.types.ts - Updated Entity, AddParams, UpdateParams, Result interfaces
- src/brainy.ts - Updated implementation and JSDoc for all affected methods
- tests/integration/entity-confidence-weight.test.ts - 16 comprehensive tests
- docs/API_REFERENCE.md - Updated with v4.3.0 examples
- src/importers/VFSStructureGenerator.ts - VFS fix
- src/vfs/VirtualFileSystem.ts - Improved error messages
- examples/unified-import-example.ts - Added vfs.init() example
- tests/integration/vfs-*-verification.test.ts - VFS verification tests

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/vfs/VirtualFileSystem.ts

@@ -1000,12 +1000,21 @@ export class VirtualFileSystem implements IVirtualFileSystem {
 
   private async ensureInitialized(): Promise<void> {
     if (!this.initialized) {
-      throw new Error(
-        'VFS not initialized. You must call await vfs.init() after getting the VFS instance.\n' +
-        'Example:\n' +
-        '  const vfs = brain.vfs()  // Note: vfs() is a method, not a property\n' +
-        '  await vfs.init()         // This creates the root directory\n' +
-        'See docs: https://github.com/Brainy-Technologies/brainy/blob/main/docs/vfs/QUICK_START.md'
+      throw new VFSError(
+        VFSErrorCode.EINVAL,
+        'VFS not initialized. Call await vfs.init() before using VFS operations.\n\n' +
+        '✅ After brain.import():\n' +
+        '  await brain.import(file, { vfsPath: "/imports/data" })\n' +
+        '  const vfs = brain.vfs()\n' +
+        '  await vfs.init()  // ← Required! Safe to call multiple times\n' +
+        '  const files = await vfs.readdir("/imports/data")\n\n' +
+        '✅ Direct VFS usage:\n' +
+        '  const vfs = brain.vfs()\n' +
+        '  await vfs.init()  // ← Always required before first use\n' +
+        '  await vfs.writeFile("/docs/readme.md", "Hello")\n\n' +
+        '📖 Docs: https://github.com/soulcraftlabs/brainy/blob/main/docs/vfs/QUICK_START.md',
+        '<unknown>',
+        'VFS'
       )
     }
   }