fix: exclude __words__ keyword index from corruption detection and getStats()

The __words__ keyword index stores 50-5000 entries per entity (one per
word), which inflated avg entries/entity well above the corruption
threshold of 100. This caused:

1. validateConsistency() to falsely detect corruption on every startup,
   triggering unnecessary clearAllIndexData() + rebuild() cycles
2. getStats() to log false "Metadata index may be corrupted" warnings
   and report inflated totalEntries/totalIds stats

Both methods now skip __words__ when counting, so stats and health
checks reflect metadata fields only (noun, type, createdAt, etc.).
Keyword search is unaffected since the __words__ field index itself
is not modified.

src/cli/commands/core.ts

@@ -172,7 +172,7 @@ export const coreCommands = {
         metadata
       }
 
-      // v4.3.x: Add confidence and weight if provided
+      // Add confidence and weight if provided
       if (options.confidence) {
         addParams.confidence = parseFloat(options.confidence)
       }
@@ -347,7 +347,7 @@ export const coreCommands = {
         searchParams.includeRelations = true
       }
 
-      // v4.7.0: VFS is now part of the knowledge graph (included by default)
+      // VFS is now part of the knowledge graph (included by default)
       // Users can exclude VFS with --where vfsType exists:false if needed
 
       // Triple Intelligence Fusion - custom weighting

src/cli/commands/cow.ts

@@ -312,7 +312,7 @@ ${chalk.cyan('Fork Statistics:')}
   },
 
   /**
-   * Migrate from v4.x to v5.0.0 (one-time)
+   * Migrate storage format (one-time)
    */
   async migrate(options: MigrateOptions) {
     let spinner: any = null
@@ -388,7 +388,7 @@ ${chalk.cyan('Fork Statistics:')}
 
       await oldBrain.init()
 
-      // Create new brain (v5.0.0)
+      // Create new brain
       const newBrain = new Brainy({
         storage: {
           type: 'filesystem',

src/cli/commands/neural.ts

@@ -117,7 +117,7 @@ export const neuralCommand = {
           await handleNeighborsCommand(neural, argv)
           break
         case 'path':
-          console.log(chalk.yellow('\n⚠️  Semantic path finding coming in v3.21.0'))
+          console.log(chalk.yellow('\n⚠️  Semantic path finding coming soon'))
           console.log(chalk.dim('This feature requires implementing graph traversal algorithms'))
           console.log(chalk.dim('Use "neighbors" and "hierarchy" commands to explore connections'))
           break
@@ -148,7 +148,7 @@ async function promptForAction(): Promise<string> {
       { name: '🎯 Find semantic clusters', value: 'clusters' },
       { name: '🌳 Show item hierarchy', value: 'hierarchy' },
       { name: '🕸️  Find semantic neighbors', value: 'neighbors' },
-      { name: '🛣️  Find semantic path between items (v3.21.0)', value: 'path', disabled: true },
+      { name: '🛣️  Find semantic path between items (coming soon)', value: 'path', disabled: true },
       { name: '🚨 Detect outliers', value: 'outliers' },
       { name: '📊 Generate visualization data', value: 'visualize' }
     ]

src/cli/commands/storage.ts

@@ -1,5 +1,5 @@
 /**
- * 💾 Storage Management Commands - v4.0.0
+ * 💾 Storage Management Commands
  *
  * Modern interactive CLI for storage lifecycle, cost optimization, and management
  */

src/cli/commands/utility.ts

@@ -133,7 +133,7 @@ export const utilityCommands = {
       // removeOrphans and rebuildIndex would require new Brainy APIs
       if (options.removeOrphans || options.rebuildIndex) {
         spinner.warn('Advanced cleanup options not yet implemented')
-        console.log(chalk.yellow('\n⚠️  Advanced cleanup features coming in v3.21.0:'))
+        console.log(chalk.yellow('\n⚠️  Advanced cleanup features coming soon:'))
         console.log(chalk.dim('  • --remove-orphans: Remove disconnected items'))
         console.log(chalk.dim('  • --rebuild-index: Rebuild vector index'))
         console.log(chalk.dim('\nUse "brainy clean" without options to clear the database'))

src/cli/commands/vfs.ts

@@ -21,7 +21,7 @@ let brainyInstance: Brainy | null = null
 const getBrainy = async (): Promise<Brainy> => {
   if (!brainyInstance) {
     brainyInstance = new Brainy()
-    await brainyInstance.init()  // v5.0.1: Initialize brain (VFS auto-initialized here!)
+    await brainyInstance.init()  // Initialize brain (VFS auto-initialized here!)
   }
   return brainyInstance
 }
@@ -52,8 +52,8 @@ export const vfsCommands = {
     const spinner = ora('Reading file...').start()
 
     try {
-      const brain = await getBrainy()  // v5.0.1: Await async getBrainy
-      // v5.0.1: VFS auto-initialized, no need for vfs.init()
+      const brain = await getBrainy()  // Await async getBrainy
+      // VFS auto-initialized, no need for vfs.init()
       const buffer = await brain.vfs.readFile(path, {
         encoding: options.encoding as any
       })

src/cli/index.ts

@@ -68,7 +68,7 @@ ${chalk.cyan('Examples:')}
   $ brainy vfs search "React components"
   $ brainy vfs similar /code/Button.tsx
 
-  ${chalk.dim('# Storage management (v4.0.0)')}
+  ${chalk.dim('# Storage management')}
   $ brainy storage status --quota
   $ brainy storage lifecycle set ${chalk.dim('# Interactive mode')}
   $ brainy storage cost-estimate
@@ -217,11 +217,11 @@ program
 
 program
   .command('path <from> <to>')
-  .description('Find semantic path between items (v3.21.0)')
+  .description('Find semantic path between items')
   .option('--steps', 'Show step-by-step path')
   .option('--max-hops <number>', 'Maximum path length', '5')
   .action(() => {
-    console.log(chalk.yellow('\n⚠️  Semantic path finding coming in v3.21.0'))
+    console.log(chalk.yellow('\n⚠️  Semantic path finding coming soon'))
     console.log(chalk.dim('This feature requires implementing graph traversal algorithms'))
     console.log(chalk.dim('Use "brainy neighbors" and "brainy hierarchy" to explore connections'))
   })
@@ -446,7 +446,7 @@ program
     vfsCommands.tree(path, options)
   })
 
-// ===== Storage Management Commands (v4.0.0) =====
+// ===== Storage Management Commands =====
 
 program
   .command('storage')
@@ -610,7 +610,7 @@ program
   .option('--iterations <n>', 'Number of iterations', '100')
   .action(utilityCommands.benchmark)
 
-// ===== COW Commands (v5.0.0) - Instant Fork & Branching =====
+// ===== COW Commands - Instant Fork & Branching =====
 
 program
   .command('fork [name]')

src/cli/interactive.ts

@@ -625,7 +625,7 @@ export async function promptCommand(): Promise<string> {
  */
 export async function startInteractiveMode() {
   console.log(chalk.cyan('\n🧠 Brainy Interactive Mode\n'))
-  console.log(chalk.yellow('Interactive REPL mode coming in v3.20.0\n'))
+  console.log(chalk.yellow('Interactive REPL mode coming soon\n'))
   console.log(chalk.dim('Use specific commands for now: brainy add, brainy search, etc.'))
   process.exit(0)
 }