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/types/agents.ts

@@ -51,23 +51,15 @@ export type AgentValidatorMap = Record<AgentName, AgentValidator>;
 
 export type McpAgentMapping = Record<PromptName, PlaywrightAgent>;
 
-export type AgentPhase =
-  | 'pre-recon'
-  | 'recon'
-  | 'vuln'
-  | 'exploit'
-  | 'report';
-
-export interface AgentDefinition {
-  name: AgentName;
-  promptName: PromptName;
-  phase: AgentPhase;
-  dependencies?: AgentName[];
-}
-
 export type AgentStatus =
   | 'pending'
   | 'in_progress'
   | 'completed'
   | 'failed'
   | 'rolled-back';
+
+export interface AgentDefinition {
+  name: AgentName;
+  displayName: string;
+  prerequisites: AgentName[];
+}

src/types/index.ts

@@ -10,5 +10,4 @@
 
 export * from './errors.js';
 export * from './config.js';
-export * from './session.js';
 export * from './agents.js';

src/types/session.ts

@@ -1,63 +0,0 @@
-// Copyright (C) 2025 Keygraph, Inc.
-//
-// This program is free software: you can redistribute it and/or modify
-// it under the terms of the GNU Affero General Public License version 3
-// as published by the Free Software Foundation.
-
-/**
- * Session type definitions
- */
-
-import type { AgentName, AgentStatus } from './agents.js';
-
-export type PhaseName =
-  | 'pre-reconnaissance'
-  | 'reconnaissance'
-  | 'vulnerability-analysis'
-  | 'exploitation'
-  | 'reporting';
-
-export interface AgentInfo {
-  name: AgentName;
-  displayName: string;
-  phase: PhaseName;
-  order: number;
-  prerequisites: AgentName[];
-}
-
-export type AgentDefinitions = Record<AgentName, AgentInfo>;
-
-export type PhaseDefinitions = Record<PhaseName, AgentName[]>;
-
-export interface AgentState {
-  status: AgentStatus;
-  startedAt?: string;
-  completedAt?: string;
-  error?: string;
-  attempts?: number;
-}
-
-export interface Session {
-  id: string;
-  targetUrl: string;
-  repoPath: string;
-  configPath?: string;
-  createdAt: string;
-  updatedAt: string;
-  completedAgents: AgentName[];
-  agentStates: Record<AgentName, AgentState>;
-  checkpoints: Record<AgentName, string>;
-}
-
-export interface SessionStore {
-  sessions: Record<string, Session>;
-}
-
-export interface SessionSummary {
-  id: string;
-  targetUrl: string;
-  repoPath: string;
-  createdAt: string;
-  completedAgents: number;
-  totalAgents: number;
-}