feat: complete VFS with Knowledge Layer integration

- Add importFile() method for single file imports
- Implement entity helper methods (linkEntities, findEntityOccurrences)
- Fix critical embedding tokenizer bug (char.charCodeAt error)
- Fix removeRelationship to actually remove using brain.unrelate()
- Add setMetadata/getMetadata methods
- Fix GitBridge to query real relationships and events
- Enable background Knowledge Layer processing
- Rewrite README to emphasize knowledge over files
- Add comprehensive VFS documentation (core, knowledge layer, examples)
- Add complete test suite covering all VFS methods

This completes the VFS implementation with full Knowledge Layer support,
enabling files as living knowledge that understand themselves, evolve
over time, and connect to everything related.

src/cli/catalog.ts

@@ -6,7 +6,7 @@
  */
 
 import chalk from 'chalk'
-import { readFileSync, writeFileSync, existsSync } from 'node:fs'
+import { readFileSync, writeFileSync, existsSync, mkdirSync } from 'node:fs'
 import { join } from 'node:path'
 import { homedir } from 'node:os'
 
@@ -302,7 +302,7 @@ function saveCache(catalog: Catalog): void {
   try {
     const dir = join(homedir(), '.brainy')
     if (!existsSync(dir)) {
-      require('fs').mkdirSync(dir, { recursive: true })
+      mkdirSync(dir, { recursive: true })
     }
     
     writeFileSync(CACHE_PATH, JSON.stringify({