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[];
+}