refactor: consolidate skill docs, add anti-drift tests, and apply audit fixes

DLO-13: Restructure vlm-library-workflow skill as safety contract layer.
- Rewrite SKILL.md (69 lines): safety contract, execution threshold semantics,
  six-step high-risk loop, decision rules, phase skeleton
- Delete redundant references (cli-reference, workflow, command-recipes, dev-guide)
- Add triage.md (failure mapping + preflight) and dev-map.md (module→test mapping)
- Add tests/test_docs_consistency.py: 78 parametrized tests verifying documented
  vlm commands exist in CLI registry
- Add CSV path mismatch test to test_plan_review.py (4th safety gate path)
- Delete vlm-expert.skill (Gemini package, 7 months stale) and README Gemini section

DLO-2 audit fixes: rate limiter injection, symmetric quarantine categories,
review-plan safety gates, parser improvements, planner validation.

CLI modularization: commands/ directory with one module per command group.

README.md

@@ -814,23 +814,6 @@ Always keep backups of important files!
 - **Local files only**: Designed for local or mounted network storage
 - **Best-effort rollback**: Rollback may not succeed if files have been modified
 
-## Agent skills
-
-This project includes workflow guidance under `skills/vlm-library-workflow/` (scan → parse → enrich → analyze → plan → review-plan → apply-review → execute).
-
-### Activation (Gemini CLI)
-
-```bash
-activate_skill vlm-library-workflow
-```
-
-### Features
-
-- **Context-Aware Guidance**: The Agent understands the VLM safety-first workflow and configuration.
-- **Risk Warnings**: Automatic alerts if a plan contains high-risk operations (>20% quarantine).
-- **Command Recipes**: Instant access to complex command sequences and troubleshooting steps.
-- **Developer Verification**: Built-in test execution recipes for verifying core logic changes.
-
 ## Development
 
 ### Running Tests
@@ -860,7 +843,8 @@ uv run pytest --cov=vlm tests/
 
 ```
 src/vlm/
-├── cli.py              # Click-based CLI interface, global options
+├── cli.py              # Thin Click registrar; global options and command registration
+├── cli_helpers.py      # Shared CLI helpers (context init, command runner, report emission)
 ├── context.py          # CLIContext and pass_context for commands
 ├── cli_helpers.py      # Shared CLI helpers
 ├── commands/           # Command implementations
@@ -894,6 +878,7 @@ src/vlm/
 ├── review_tui.py       # Optional Textual review UI
 ├── transaction.py    # Execution transaction log
 ├── executor.py         # File operations and rollback
+├── transaction.py      # Transaction/rollback logging for executed operations
 ├── quarantine.py       # Quarantine management
 ├── state.py            # File state tracking
 ├── reports.py          # Report generation