chore: recovery checkpoint - v3.0 API successfully recovered

CRITICAL CHECKPOINT - DO NOT PUSH TO GITHUB

Recovery Status:
- Successfully recovered brainy.ts from compiled JavaScript
- All core v3.0 API methods functional (add, get, update, delete, relate, find, etc.)
- Neural subsystem intact (562KB embedded patterns, NLP working)
- Augmentation pipeline operational (20+ augmentations)
- HNSW clustering system complete
- Triple Intelligence compiled (needs constructor fix)
- Test suite validates functionality

Changes preserved:
- 898 files with changes from last 3 days
- 144,475 insertions
- All augmentation improvements
- All test coverage enhancements
- Complete v3.0 feature set

This is a LOCAL checkpoint only - contains recovered work after corruption incident.
Created backup in .backups/brainy-full-20250910-151314.tar.gz

Branch: recovery-checkpoint-20250910-151433
Date: Wed Sep 10 03:18:04 PM PDT 2025

.recovery-workspace/dist-backup-20250910-141917/cli/index.js

@@ -0,0 +1,167 @@
+#!/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 { 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) {
+    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();
+}
+//# sourceMappingURL=index.js.map