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/audit-session.ts

@@ -155,21 +155,6 @@ export class AuditSession {
     }
   }
 
-  /**
-   * Mark multiple agents as rolled back
-   */
-  async markMultipleRolledBack(agentNames: string[]): Promise<void> {
-    await this.ensureInitialized();
-
-    const unlock = await sessionMutex.lock(this.sessionId);
-    try {
-      await this.metricsTracker.reload();
-      await this.metricsTracker.markMultipleRolledBack(agentNames);
-    } finally {
-      unlock();
-    }
-  }
-
   /**
    * Update session status
    */