CHECKPOINT: Brainy 2.0 API refactor - pre-fixes state

Current state:
- Unified augmentation system to BrainyAugmentation interface
- Changed methods to specific noun/verb naming (addNoun, getNoun, etc)
- Made old methods private
- Combined getNouns into single unified method
- Neural API exists and is complete
- Triple Intelligence uses correct Brainy operators (not MongoDB)

Issues identified:
- Documentation incorrectly shows MongoDB operators (code is correct)
- Need to ensure all features are properly exposed
- Need to verify nothing was lost in simplification

This commit serves as a rollback point before applying fixes.

src/cli/index.ts

@@ -0,0 +1,199 @@
+#!/usr/bin/env node
+
+/**
+ * Brainy CLI - Enterprise Neural Intelligence System
+ * 
+ * Full TypeScript implementation with type safety and shared code
+ */
+
+import { Command } from 'commander'
+import chalk from 'chalk'
+import ora from 'ora'
+import { BrainyData } from '../brainyData.js'
+import { neuralCommands } from './commands/neural.js'
+import { coreCommands } from './commands/core.js'
+import { utilityCommands } from './commands/utility.js'
+import { version } from '../package.json'
+
+// CLI Configuration
+const program = new Command()
+
+program
+  .name('brainy')
+  .description('🧠 Enterprise Neural Intelligence Database')
+  .version(version)
+  .option('-v, --verbose', 'Verbose output')
+  .option('--json', 'JSON output format')
+  .option('--pretty', 'Pretty JSON output')
+  .option('--no-color', 'Disable colored output')
+
+// ===== Core Commands =====
+
+program
+  .command('add <text>')
+  .description('Add text or JSON to the neural database')
+  .option('-i, --id <id>', 'Specify custom ID')
+  .option('-m, --metadata <json>', 'Add metadata')
+  .option('-t, --type <type>', 'Specify noun type')
+  .action(coreCommands.add)
+
+program
+  .command('search <query>')
+  .description('Search the neural database')
+  .option('-k, --limit <number>', 'Number of results', '10')
+  .option('-t, --threshold <number>', 'Similarity threshold')
+  .option('--metadata <json>', 'Filter by metadata')
+  .action(coreCommands.search)
+
+program
+  .command('get <id>')
+  .description('Get item by ID')
+  .option('--with-connections', 'Include connections')
+  .action(coreCommands.get)
+
+program
+  .command('relate <source> <verb> <target>')
+  .description('Create a relationship between items')
+  .option('-w, --weight <number>', 'Relationship weight')
+  .option('-m, --metadata <json>', 'Relationship metadata')
+  .action(coreCommands.relate)
+
+program
+  .command('import <file>')
+  .description('Import data from file')
+  .option('-f, --format <format>', 'Input format (json|csv|jsonl)', 'json')
+  .option('--batch-size <number>', 'Batch size for import', '100')
+  .action(coreCommands.import)
+
+program
+  .command('export [file]')
+  .description('Export database')
+  .option('-f, --format <format>', 'Output format (json|csv|jsonl)', 'json')
+  .action(coreCommands.export)
+
+// ===== Neural Commands =====
+
+program
+  .command('similar <a> <b>')
+  .alias('sim')
+  .description('Calculate similarity between two items')
+  .option('--explain', 'Show detailed explanation')
+  .option('--breakdown', 'Show similarity breakdown')
+  .action(neuralCommands.similar)
+
+program
+  .command('cluster')
+  .alias('clusters')
+  .description('Find semantic clusters in the data')
+  .option('--algorithm <type>', 'Clustering algorithm (hierarchical|kmeans|dbscan)', 'hierarchical')
+  .option('--threshold <number>', 'Similarity threshold', '0.7')
+  .option('--min-size <number>', 'Minimum cluster size', '2')
+  .option('--max-clusters <number>', 'Maximum number of clusters')
+  .option('--near <query>', 'Find clusters near a query')
+  .option('--show', 'Show visual representation')
+  .action(neuralCommands.cluster)
+
+program
+  .command('related <id>')
+  .alias('neighbors')
+  .description('Find semantically related items')
+  .option('-l, --limit <number>', 'Number of results', '10')
+  .option('-r, --radius <number>', 'Semantic radius', '0.3')
+  .option('--with-scores', 'Include similarity scores')
+  .option('--with-edges', 'Include connections')
+  .action(neuralCommands.related)
+
+program
+  .command('hierarchy <id>')
+  .alias('tree')
+  .description('Show semantic hierarchy for an item')
+  .option('-d, --depth <number>', 'Hierarchy depth', '3')
+  .option('--parents-only', 'Show only parent hierarchy')
+  .option('--children-only', 'Show only child hierarchy')
+  .action(neuralCommands.hierarchy)
+
+program
+  .command('path <from> <to>')
+  .description('Find semantic path between items')
+  .option('--steps', 'Show step-by-step path')
+  .option('--max-hops <number>', 'Maximum path length', '5')
+  .action(neuralCommands.path)
+
+program
+  .command('outliers')
+  .alias('anomalies')
+  .description('Detect semantic outliers')
+  .option('-t, --threshold <number>', 'Outlier threshold', '0.3')
+  .option('--explain', 'Explain why items are outliers')
+  .action(neuralCommands.outliers)
+
+program
+  .command('visualize')
+  .alias('viz')
+  .description('Generate visualization data')
+  .option('-f, --format <format>', 'Output format (json|d3|graphml)', 'json')
+  .option('--max-nodes <number>', 'Maximum nodes', '500')
+  .option('--dimensions <number>', '2D or 3D', '2')
+  .option('-o, --output <file>', 'Output file')
+  .action(neuralCommands.visualize)
+
+// ===== Utility Commands =====
+
+program
+  .command('stats')
+  .alias('statistics')
+  .description('Show database statistics')
+  .option('--by-service', 'Group by service')
+  .option('--detailed', 'Show detailed stats')
+  .action(utilityCommands.stats)
+
+program
+  .command('clean')
+  .description('Clean and optimize database')
+  .option('--remove-orphans', 'Remove orphaned items')
+  .option('--rebuild-index', 'Rebuild search index')
+  .action(utilityCommands.clean)
+
+program
+  .command('benchmark')
+  .alias('bench')
+  .description('Run performance benchmarks')
+  .option('--operations <ops>', 'Operations to benchmark', 'all')
+  .option('--iterations <n>', 'Number of iterations', '100')
+  .action(utilityCommands.benchmark)
+
+// ===== Interactive Mode =====
+
+program
+  .command('interactive')
+  .alias('i')
+  .description('Start interactive REPL mode')
+  .action(async () => {
+    const { startInteractiveMode } = await import('./interactive.js')
+    await startInteractiveMode()
+  })
+
+// ===== Error Handling =====
+
+program.exitOverride()
+
+try {
+  await program.parseAsync(process.argv)
+} catch (error: any) {
+  if (error.code === 'commander.helpDisplayed') {
+    process.exit(0)
+  }
+  
+  console.error(chalk.red('Error:'), error.message)
+  
+  if (program.opts().verbose) {
+    console.error(chalk.gray(error.stack))
+  }
+  
+  process.exit(1)
+}
+
+// Handle no command
+if (!process.argv.slice(2).length) {
+  program.outputHelp()
+}