refactor: remove orchestration layer (#45)

* refactor: remove orchestration layer and simplify CLI

Remove the complex orchestration layer including checkpoint management,
rollback/recovery commands, and session management commands. This
consolidates the execution logic directly in shannon.ts for a simpler
fire-and-forget execution model.

Changes:
- Remove checkpoint-manager.ts and rollback functionality
- Remove command-handler.ts and cli/prompts.ts
- Simplify session-manager.ts to just agent definitions
- Consolidate orchestration logic in shannon.ts
- Update CLAUDE.md documentation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor: move session lock logic to shannon.ts, simplify session-manager

- Reduce session-manager.ts to only AGENTS, AGENT_ORDER, getParallelGroups()
- Move Session interface and lock file functions to shannon.ts
- Simplify Session to only: id, webUrl, repoPath, status, startedAt
- Remove unused types/session.ts

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* refactor: use crypto.randomUUID() for session ID generation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

src/audit/metrics-tracker.ts

@@ -20,7 +20,6 @@ import {
   calculatePercentage,
   type SessionMetadata,
 } from './utils.js';
-import type { AgentName, PhaseName } from '../types/index.js';
 
 interface AttemptData {
   attempt_number: number;
@@ -32,12 +31,11 @@ interface AttemptData {
 }
 
 interface AgentMetrics {
-  status: 'in-progress' | 'success' | 'failed' | 'rolled-back';
+  status: 'in-progress' | 'success' | 'failed';
   attempts: AttemptData[];
   final_duration_ms: number;
   total_cost_usd: number;
   checkpoint?: string;
-  rolled_back_at?: string;
 }
 
 interface PhaseMetrics {
@@ -208,42 +206,6 @@ export class MetricsTracker {
     await this.save();
   }
 
-  /**
-   * Mark agent as rolled back
-   */
-  async markRolledBack(agentName: string): Promise<void> {
-    if (!this.data || !this.data.metrics.agents[agentName]) {
-      return; // Agent not tracked
-    }
-
-    const agent = this.data.metrics.agents[agentName]!;
-    agent.status = 'rolled-back';
-    agent.rolled_back_at = formatTimestamp();
-
-    // Recalculate aggregations (exclude rolled-back agents)
-    this.recalculateAggregations();
-
-    await this.save();
-  }
-
-  /**
-   * Mark multiple agents as rolled back
-   */
-  async markMultipleRolledBack(agentNames: string[]): Promise<void> {
-    if (!this.data) return;
-
-    for (const agentName of agentNames) {
-      if (this.data.metrics.agents[agentName]) {
-        const agent = this.data.metrics.agents[agentName]!;
-        agent.status = 'rolled-back';
-        agent.rolled_back_at = formatTimestamp();
-      }
-    }
-
-    this.recalculateAggregations();
-    await this.save();
-  }
-
   /**
    * Update session status
    */
@@ -267,7 +229,7 @@ export class MetricsTracker {
 
     const agents = this.data.metrics.agents;
 
-    // Only count successful agents (not rolled-back or failed)
+    // Only count successful agents
     const successfulAgents = Object.entries(agents).filter(
       ([, data]) => data.status === 'success'
     );