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>

README.md

@@ -286,14 +286,6 @@ rules:
 
 If your application uses two-factor authentication, simply add the TOTP secret to your config file. The AI will automatically generate the required codes during testing.
 
-### Check Status
-
-View progress of previous runs:
-
-```bash
-docker run --rm shannon:latest --status
-```
-
 ### Output and Results
 
 All results are saved to `./audit-logs/` by default. Use `--output <path>` to specify a custom directory. If using `--output`, ensure that path is mounted to an accessible host directory (e.g., `-v "$(pwd)/custom-directory:/app/reports"`).