// src/v3/core/secure-foundation.ts
import { createSecureHash, generateToken, validatePath } from './security';

export class SecureFoundation {
  // Secure password hashing (replaces SHA-256 with hardcoded salt)
  async hashPassword(password: string): Promise<string> {
    const bcrypt = await import('bcrypt');
    return bcrypt.hash(password, 12);
  }

  // Secure token generation (replaces Math.random())
  generateSecureToken(length = 32): string {
    return crypto.randomBytes(length).toString('hex');
  }

  // Path validation (prevents traversal)
  validateFilePath(userPath: string, baseDir: string): string {
    const resolved = path.resolve(baseDir, userPath);
    if (!resolved.startsWith(path.resolve(baseDir))) {
      throw new SecurityError('Path traversal detected');
    }
    return resolved;
  }

  // Safe process execution (no shell injection)
  async safeExec(command: string, args: string[]): Promise<ExecResult> {
    return execFile(command, args, { shell: false });
  }
}

// package.json - Updated secure dependencies
{
  "dependencies": {
    "@anthropic-ai/claude-code": "^2.0.31",
    "@modelcontextprotocol/sdk": "^1.24.0",
    "agentic-flow": "^2.0.1-alpha.0",
    "bcrypt": "^5.1.1",
    "zod": "^3.22.0"
  }
}

// src/v3/validation/schemas.ts
import { z } from 'zod';

export const InitConfigSchema = z.object({
  mode: z.enum(['standard', 'sparc', 'hive-mind', 'neural', 'github', 'enterprise']),
  agenticFlow: z.object({
    enabled: z.boolean().default(true),
    sona: z.enum(['real-time', 'balanced', 'research', 'edge', 'batch']).default('balanced'),
    attention: z.enum(['flash', 'multi-head', 'linear', 'hyperbolic', 'moe']).default('flash'),
    learning: z.boolean().default(true)
  }).optional(),
  security: z.object({
    validatePaths: z.boolean().default(true),
    sanitizeInputs: z.boolean().default(true)
  }).default({})
});

export type InitConfig = z.infer<typeof InitConfigSchema>;

// src/v3/speed/flash-attention-coordinator.ts
import { EnhancedAgentDBWrapper, AttentionCoordinator } from 'agentic-flow/core';

export class FlashCoordinator {
  private wrapper: EnhancedAgentDBWrapper;
  private attention: AttentionCoordinator;

  constructor() {
    this.wrapper = new EnhancedAgentDBWrapper({
      enableAttention: true,
      attentionConfig: {
        type: 'flash',           // 2.49x-7.47x speedup
        memoryEfficient: true,   // 50-75% memory reduction
        batchSize: 64
      },
      runtimePreference: 'napi'  // Fastest: NAPI → WASM → JS fallback
    });
  }

  async initialize(): Promise<void> {
    await this.wrapper.initialize();
    this.attention = new AttentionCoordinator(
      this.wrapper.getAttentionService()
    );
  }

  // Fast agent coordination with consensus
  async coordinateAgents(outputs: AgentOutput[]): Promise<Consensus> {
    return this.attention.coordinateAgents(outputs, 'flash');
  }

  // Fast pattern search with HNSW indexing (150x-12,500x faster)
  async searchPatterns(query: string, k = 5): Promise<Pattern[]> {
    return this.wrapper.gnnEnhancedSearch(query, { k });
  }
}

// src/v3/init/lazy-loader.ts
export class LazyInitializer {
  private static instances = new Map<string, any>();
  private static initializing = new Map<string, Promise<any>>();

  static async get<T>(key: string, factory: () => Promise<T>): Promise<T> {
    // Return cached instance
    if (this.instances.has(key)) {
      return this.instances.get(key);
    }

    // Wait for in-progress initialization
    if (this.initializing.has(key)) {
      return this.initializing.get(key);
    }

    // Initialize once
    const promise = factory().then(instance => {
      this.instances.set(key, instance);
      this.initializing.delete(key);
      return instance;
    });

    this.initializing.set(key, promise);
    return promise;
  }
}

// Usage - components only initialize when needed
export const getFlashCoordinator = () =>
  LazyInitializer.get('flash', async () => {
    const coord = new FlashCoordinator();
    await coord.initialize();
    return coord;
  });

export const getAgentDB = () =>
  LazyInitializer.get('agentdb', async () => {
    const db = new AgentDBWrapper();
    await db.initialize();
    return db;
  });

// src/v3/learning/sona-manager.ts
export interface SONAConfig {
  profile: 'real-time' | 'balanced' | 'research' | 'edge' | 'batch';
  reflexion: boolean;
  skillLibrary: boolean;
  continualLearning: boolean;
}

export class SONAManager {
  private adapter: AgenticFlowAdapter;
  private config: SONAConfig;

  constructor(config: Partial<SONAConfig> = {}) {
    this.config = {
      profile: config.profile ?? 'balanced',
      reflexion: config.reflexion ?? true,
      skillLibrary: config.skillLibrary ?? true,
      continualLearning: config.continualLearning ?? true
    };
  }

  async initialize(): Promise<void> {
    this.adapter = new AgenticFlowAdapter({
      sona: this.config.profile,
      learning: true
    });
    await this.adapter.initialize();
  }

  // Learn from successful operations
  async learn(context: LearningContext): Promise<void> {
    const reward = this.calculateReward(context);

    await this.adapter.storePattern(
      context.operation,
      context.result,
      reward,
      { algorithm: 'ppo' }
    );

    // Add to skill library if high quality
    if (reward > 0.8 && this.config.skillLibrary) {
      await this.adapter.addToSkillLibrary(
        context.agentId,
        context.taskType,
        context.output
      );
    }
  }

  // Reflexion: self-improvement through feedback
  async reflect(agentId: string, task: Task, result: TaskResult): Promise<Improvement[]> {
    if (!this.config.reflexion) return [];

    const pastAttempts = await this.adapter.searchPatterns(
      `${agentId}:${task.type}`,
      { k: 10 }
    );

    const improvements = await this.adapter.analyzeForImprovement(
      pastAttempts,
      result
    );

    return improvements;
  }

  private calculateReward(context: LearningContext): number {
    let reward = context.success ? 0.7 : 0.0;

    if (context.metrics?.quality) reward += context.metrics.quality * 0.2;
    if (context.metrics?.speed) reward += context.metrics.speed * 0.1;

    return Math.min(reward, 1.0);
  }
}

// src/v3/learning/learning-hooks.ts
export class LearningHooks {
  private sona: SONAManager;

  constructor(sona: SONAManager) {
    this.sona = sona;
  }

  // Pre-task: Query learned patterns
  async preTask(context: HookContext): Promise<void> {
    const patterns = await this.sona.searchPatterns(context.taskDescription);

    if (patterns.length > 0) {
      context.suggestions = patterns.map(p => ({
        approach: p.pattern,
        confidence: p.score,
        source: 'learned'
      }));
    }
  }

  // Post-task: Store learning
  async postTask(context: HookContext): Promise<void> {
    await this.sona.learn({
      operation: context.taskId,
      result: context.result,
      success: context.success,
      agentId: context.agentId,
      taskType: context.taskType,
      output: context.output,
      metrics: context.metrics
    });

    // Trigger reflexion for improvement
    if (context.success) {
      const improvements = await this.sona.reflect(
        context.agentId,
        context.task,
        context.result
      );

      if (improvements.length > 0) {
        await this.applyImprovements(context.agentId, improvements);
      }
    }
  }

  // Post-edit: Learn from code changes
  async postEdit(context: HookContext): Promise<void> {
    if (context.success) {
      await this.sona.learn({
        operation: `edit:${context.file}`,
        result: context.changes,
        success: true,
        agentId: context.agentId || 'default',
        taskType: 'code-edit',
        output: context.newContent
      });
    }
  }
}

// src/v3/learning/reasoningbank-bridge.ts
export class ReasoningBankBridge {
  private agentDB: AgentDBWrapper;

  async storeTrajectory(trajectory: Trajectory): Promise<void> {
    // Store with embedding for semantic search
    await this.agentDB.store({
      key: `trajectory:${trajectory.id}`,
      value: trajectory,
      embedding: await this.embed(trajectory.description),
      metadata: {
        success: trajectory.success,
        reward: trajectory.reward,
        timestamp: Date.now()
      }
    });
  }

  async queryBestApproach(task: string): Promise<Trajectory[]> {
    // GNN-enhanced search for similar successful trajectories
    const results = await this.agentDB.gnnEnhancedSearch(task, {
      k: 5,
      filter: { success: true },
      minReward: 0.7
    });

    return results.map(r => r.value as Trajectory);
  }
}

// src/v3/compatibility/v2-api.ts
import { FlashCoordinator } from '../speed/flash-attention-coordinator';
import { SONAManager } from '../learning/sona-manager';

/**
 * Complete v2 API compatibility
 * All existing code works unchanged
 */

// v2 SwarmCoordinator - fully preserved
export class SwarmCoordinator {
  private v3Flash: FlashCoordinator;
  private v3Sona: SONAManager;
  private eventEmitter = new EventEmitter();

  constructor(config?: V2Config) {
    // v3 enhancements transparent to v2 callers
    this.v3Flash = new FlashCoordinator();
    this.v3Sona = new SONAManager({ profile: 'balanced' });
  }

  async initialize(): Promise<void> {
    await Promise.all([
      this.v3Flash.initialize(),
      this.v3Sona.initialize()
    ]);
  }

  // v2 method signature preserved exactly
  async spawnAgent(profile: AgentProfile): Promise<string> {
    // Internally uses v3 with learning
    const agentId = await this.v3Flash.spawnAgent(profile.type, {
      learning: true,  // v3 enhancement
      ...profile
    });

    this.eventEmitter.emit('agent:spawned', { agentId, profile });
    return agentId;
  }

  // v2 method signature preserved exactly
  async assignTask(task: Task): Promise<void> {
    await this.v3Flash.executeTask(task);
    this.eventEmitter.emit('task:assigned', { task });
  }

  // v2 event system preserved
  on(event: string, handler: (...args: any[]) => void): void {
    this.eventEmitter.on(event, handler);
  }

  off(event: string, handler: (...args: any[]) => void): void {
    this.eventEmitter.off(event, handler);
  }
}

// v2 AgentManager - fully preserved
export class AgentManager {
  private v3: EnhancedAgentManager;

  // All v2 methods work exactly as before
  async createAgent(template: string): Promise<string> {
    return this.v3.createAgentWithLearning(template);
  }

  async getAgent(id: string): Promise<Agent | undefined> {
    return this.v3.getAgent(id);
  }

  async terminateAgent(id: string): Promise<void> {
    return this.v3.terminateAgent(id);
  }
}

// v2 MemoryManager - fully preserved
export class MemoryManager {
  private v3: HybridMemorySystem;

  async store(key: string, value: any): Promise<void> {
    return this.v3.store(key, value);
  }

  async retrieve(key: string): Promise<any> {
    return this.v3.retrieve(key);
  }

  async search(query: string): Promise<any[]> {
    return this.v3.search(query);
  }
}

// src/v3/compatibility/config-migration.ts
export async function autoMigrateConfig(): Promise<void> {
  const configPath = '.claude/config.json';

  if (!await fileExists(configPath)) {
    // Fresh install - create v3 config
    await createDefaultV3Config(configPath);
    return;
  }

  const config = await loadConfig(configPath);

  // Already v3
  if (config.version === '3.0.0') return;

  // Migrate v2 to v3
  const v3Config = {
    version: '3.0.0',

    // Preserve all v2 settings
    ...config,

    // Add v3 enhancements
    agenticFlow: {
      enabled: true,
      attention: 'flash',
      sona: 'balanced',
      learning: true
    },

    // Migrate hooks to single source
    hooks: consolidateHooks(config)
  };

  // Backup v2 config
  await fs.copyFile(configPath, `${configPath}.v2.backup`);

  // Save v3 config
  await saveConfig(configPath, v3Config);

  console.log('✅ Configuration migrated to v3');
}

// src/v3/init/init-controller.ts
import { SecureFoundation } from '../core/secure-foundation';
import { FlashCoordinator } from '../speed/flash-attention-coordinator';
import { SONAManager } from '../learning/sona-manager';
import { InitConfigSchema, InitConfig } from '../validation/schemas';

export class InitController {
  private security: SecureFoundation;
  private flash: FlashCoordinator;
  private sona: SONAManager;
  private config: InitConfig;

  constructor(config: Partial<InitConfig> = {}) {
    // Validate config with Zod
    this.config = InitConfigSchema.parse(config);

    this.security = new SecureFoundation();
    this.flash = new FlashCoordinator();
    this.sona = new SONAManager(this.config.agenticFlow);
  }

  async initialize(): Promise<InitResult> {
    const startTime = Date.now();
    const results: InitStepResult[] = [];

    try {
      // Step 1: Security initialization
      results.push(await this.initSecurity());

      // Step 2: Directory structure
      results.push(await this.initDirectories());

      // Step 3: agentic-flow integration
      results.push(await this.initAgenticFlow());

      // Step 4: Mode-specific initialization
      results.push(await this.initMode());

      // Step 5: Learning system
      results.push(await this.initLearning());

      // Step 6: Backward compatibility check
      results.push(await this.initCompatibility());

      return {
        success: true,
        mode: this.config.mode,
        duration: Date.now() - startTime,
        steps: results,
        capabilities: this.getCapabilities()
      };
    } catch (error) {
      return {
        success: false,
        error: error.message,
        duration: Date.now() - startTime,
        steps: results
      };
    }
  }

  private async initSecurity(): Promise<InitStepResult> {
    // Validate environment
    await this.security.validateEnvironment();

    // Check for secure token
    if (!process.env.CLAUDE_FLOW_TOKEN) {
      const token = this.security.generateSecureToken();
      console.log('Generated secure token - add to environment');
    }

    return { step: 'security', success: true };
  }

  private async initDirectories(): Promise<InitStepResult> {
    const dirs = [
      '.claude',
      '.claude/agents',
      '.claude/commands',
      '.claude/skills',
      '.claude/checkpoints/active',
      '.claude-flow/coordination',
      '.claude-flow/training',
      '.claude-flow/metrics'
    ];

    for (const dir of dirs) {
      await fs.mkdir(dir, { recursive: true });
    }

    return { step: 'directories', success: true };
  }

  private async initAgenticFlow(): Promise<InitStepResult> {
    if (!this.config.agenticFlow?.enabled) {
      return { step: 'agentic-flow', success: true, skipped: true };
    }

    await Promise.all([
      this.flash.initialize(),
      this.sona.initialize()
    ]);

    return { step: 'agentic-flow', success: true };
  }

  private async initMode(): Promise<InitStepResult> {
    const modeInitializers: Record<string, () => Promise<void>> = {
      'standard': () => this.initStandardMode(),
      'sparc': () => this.initSparcMode(),
      'hive-mind': () => this.initHiveMindMode(),
      'neural': () => this.initNeuralMode(),
      'github': () => this.initGitHubMode(),
      'enterprise': () => this.initEnterpriseMode()
    };

    const initializer = modeInitializers[this.config.mode];
    await initializer();

    return { step: 'mode', success: true, mode: this.config.mode };
  }

  private async initLearning(): Promise<InitStepResult> {
    // Load existing patterns
    const patterns = await this.sona.loadExistingPatterns();

    // Register learning hooks
    await this.registerLearningHooks();

    return {
      step: 'learning',
      success: true,
      patternsLoaded: patterns.length
    };
  }

  private async initCompatibility(): Promise<InitStepResult> {
    // Auto-migrate v2 config if present
    await autoMigrateConfig();

    // Verify v2 APIs work
    const v2Test = await this.testV2Compatibility();

    return { step: 'compatibility', success: v2Test.passed };
  }

  private getCapabilities(): Capabilities {
    return {
      flashAttention: this.config.agenticFlow?.attention === 'flash',
      sonaLearning: this.config.agenticFlow?.enabled,
      reflexion: this.config.agenticFlow?.enabled,
      vectorSearch: this.config.agenticFlow?.enabled,
      mode: this.config.mode,
      v2Compatible: true
    };
  }
}

// src/v3/init/modes/index.ts
export abstract class ModeInitializer {
  protected controller: InitController;
  protected sona: SONAManager;

  abstract get modeName(): string;
  abstract get requiredAgents(): string[];
  abstract get requiredSkills(): string[];

  async initialize(): Promise<void> {
    // Copy agents for this mode
    await this.copyAgents();

    // Copy skills for this mode
    await this.copySkills();

    // Copy commands for this mode
    await this.copyCommands();

    // Mode-specific setup
    await this.modeSpecificSetup();

    // Load learned patterns for this mode
    await this.loadModePatterns();
  }

  protected async loadModePatterns(): Promise<void> {
    const patterns = await this.sona.searchPatterns(
      `mode:${this.modeName}`,
      { k: 100 }
    );

    console.log(`Loaded ${patterns.length} learned patterns for ${this.modeName} mode`);
  }

  protected abstract modeSpecificSetup(): Promise<void>;
}

// Standard mode
export class StandardModeInitializer extends ModeInitializer {
  get modeName() { return 'standard'; }
  get requiredAgents() { return ['coder', 'tester', 'reviewer', 'researcher', 'planner']; }
  get requiredSkills() { return ['swarm-orchestration', 'pair-programming']; }

  protected async modeSpecificSetup(): Promise<void> {
    // Standard mode uses balanced SONA profile
    await this.sona.setProfile('balanced');
  }
}

// SPARC mode
export class SparcModeInitializer extends ModeInitializer {
  get modeName() { return 'sparc'; }
  get requiredAgents() {
    return ['sparc-coord', 'specification', 'pseudocode', 'architecture', 'refinement'];
  }
  get requiredSkills() { return ['sparc-methodology', 'tdd-london-swarm']; }

  protected async modeSpecificSetup(): Promise<void> {
    // SPARC uses research profile for higher quality
    await this.sona.setProfile('research');

    // Initialize SPARC-specific learning
    await this.initSparcPhaseMemory();
  }

  private async initSparcPhaseMemory(): Promise<void> {
    // Load patterns for each SPARC phase
    for (const phase of ['spec', 'pseudo', 'arch', 'refine', 'complete']) {
      await this.sona.searchPatterns(`sparc:${phase}`);
    }
  }
}

// Hive-Mind mode
export class HiveMindModeInitializer extends ModeInitializer {
  get modeName() { return 'hive-mind'; }
  get requiredAgents() {
    return ['queen-coordinator', 'worker-specialist', 'scout-explorer', 'swarm-memory-manager'];
  }
  get requiredSkills() { return ['hive-mind-advanced', 'collective-intelligence']; }

  protected async modeSpecificSetup(): Promise<void> {
    // Hive-mind uses real-time for fast coordination
    await this.sona.setProfile('real-time');

    // Initialize queen memory
    await this.initQueenMemory();
  }
}

// Neural mode
export class NeuralModeInitializer extends ModeInitializer {
  get modeName() { return 'neural'; }
  get requiredAgents() { return ['ml-developer', 'perf-analyzer', 'code-analyzer']; }
  get requiredSkills() { return ['flow-nexus-neural', 'reasoningbank-intelligence']; }

  protected async modeSpecificSetup(): Promise<void> {
    // Neural uses research profile for maximum learning
    await this.sona.setProfile('research');

    // Initialize neural training pipelines
    await this.initNeuralPipelines();
  }
}

// GitHub mode
export class GitHubModeInitializer extends ModeInitializer {
  get modeName() { return 'github'; }
  get requiredAgents() {
    return ['pr-manager', 'code-review-swarm', 'issue-tracker', 'release-manager'];
  }
  get requiredSkills() {
    return ['github-workflow-automation', 'github-code-review', 'github-release-management'];
  }

  protected async modeSpecificSetup(): Promise<void> {
    // GitHub mode uses balanced for general work
    await this.sona.setProfile('balanced');

    // Initialize GitHub-specific patterns
    await this.initGitHubPatterns();
  }
}

// Enterprise mode
export class EnterpriseModeInitializer extends ModeInitializer {
  get modeName() { return 'enterprise'; }
  get requiredAgents() {
    return [...StandardModeInitializer.prototype.requiredAgents,
            ...SparcModeInitializer.prototype.requiredAgents,
            ...GitHubModeInitializer.prototype.requiredAgents];
  }
  get requiredSkills() {
    return ['all'];  // All skills available
  }

  protected async modeSpecificSetup(): Promise<void> {
    // Enterprise uses research for maximum quality
    await this.sona.setProfile('research');

    // Full feature set
    await this.enableAllFeatures();
  }
}

// src/v3/cli/commands/init.ts
import { Command } from 'commander';
import { InitController } from '../init/init-controller';

export function createInitCommand(): Command {
  return new Command('init')
    .description('Initialize Claude-Flow v3 with enhanced capabilities')
    .option('-m, --mode <mode>', 'Initialization mode', 'standard')
    .option('--sona <profile>', 'SONA learning profile', 'balanced')
    .option('--no-learning', 'Disable self-learning')
    .option('--attention <type>', 'Attention mechanism', 'flash')
    .option('--migrate', 'Auto-migrate from v2')
    .action(async (options) => {
      console.log('🚀 Initializing Claude-Flow v3...\n');

      const controller = new InitController({
        mode: options.mode,
        agenticFlow: {
          enabled: true,
          sona: options.sona,
          attention: options.attention,
          learning: options.learning !== false
        }
      });

      const result = await controller.initialize();

      if (result.success) {
        console.log(`\n✅ Initialization complete in ${result.duration}ms`);
        console.log(`   Mode: ${result.mode}`);
        console.log(`   Capabilities:`);
        console.log(`   - Flash Attention: ${result.capabilities.flashAttention ? '✓' : '✗'}`);
        console.log(`   - SONA Learning: ${result.capabilities.sonaLearning ? '✓' : '✗'}`);
        console.log(`   - Reflexion: ${result.capabilities.reflexion ? '✓' : '✗'}`);
        console.log(`   - v2 Compatible: ${result.capabilities.v2Compatible ? '✓' : '✗'}`);
      } else {
        console.error(`\n❌ Initialization failed: ${result.error}`);
        process.exit(1);
      }
    });
}

# Day 1-2: Security fixes
npm update @anthropic-ai/claude-code@^2.0.31
npm update @modelcontextprotocol/sdk@^1.24.0
npm install bcrypt zod

# Day 3-4: Core foundation
# - SecureFoundation class
# - Input validation schemas
# - Path sanitization

# Day 5: Cleanup
./scripts/cleanup-v3.sh --execute

# Day 1-2: agentic-flow upgrade
npm install [email protected]

# Day 3-4: Flash Attention
# - FlashCoordinator implementation
# - Lazy initialization

# Day 5: Performance testing
npm run benchmark

# Day 1-2: SONA integration
# - SONAManager implementation
# - Profile configuration

# Day 3-4: Learning hooks
# - LearningHooks class
# - ReasoningBank bridge

# Day 5: Reflexion system
# - Self-improvement loop
# - Skill library

# Day 1-2: Init system
# - InitController
# - Mode initializers

# Day 3-4: Backward compatibility
# - v2 API wrappers
# - Config migration

# Day 5: Testing
npm run test:v3
npm run test:compatibility

# Fresh v3 installation
npx claude-flow init --mode sparc --sona research

# With all features
npx claude-flow init --mode enterprise --sona research --attention flash

# Minimal (fast startup)
npx claude-flow init --mode standard --sona real-time

# Migrate from v2
npx claude-flow init --migrate

// v3 API usage
import { InitController, SwarmCoordinator, SONAManager } from 'claude-flow/v3';

// Initialize with learning
const init = new InitController({
  mode: 'sparc',
  agenticFlow: { sona: 'research', learning: true }
});
await init.initialize();

// Use v2 API (still works!)
const coordinator = new SwarmCoordinator();
await coordinator.spawnAgent({ type: 'coder' });

// Or use v3 API directly
const sona = new SONAManager({ profile: 'research' });
const patterns = await sona.searchPatterns('implement feature');