CI/CD Integration with Ephemeral Deployment Model (#14)

* feat: Complete migration from Prefect to Temporal

BREAKING CHANGE: Replaces Prefect workflow orchestration with Temporal

## Major Changes
- Replace Prefect with Temporal for workflow orchestration
- Implement vertical worker architecture (rust, android)
- Replace Docker registry with MinIO for unified storage
- Refactor activities to be co-located with workflows
- Update all API endpoints for Temporal compatibility

## Infrastructure
- New: docker-compose.temporal.yaml (Temporal + MinIO + workers)
- New: workers/ directory with rust and android vertical workers
- New: backend/src/temporal/ (manager, discovery)
- New: backend/src/storage/ (S3-cached storage with MinIO)
- New: backend/toolbox/common/ (shared storage activities)
- Deleted: docker-compose.yaml (old Prefect setup)
- Deleted: backend/src/core/prefect_manager.py
- Deleted: backend/src/services/prefect_stats_monitor.py
- Deleted: Docker registry and insecure-registries requirement

## Workflows
- Migrated: security_assessment workflow to Temporal
- New: rust_test workflow (example/test workflow)
- Deleted: secret_detection_scan (Prefect-based, to be reimplemented)
- Activities now co-located with workflows for independent testing

## API Changes
- Updated: backend/src/api/workflows.py (Temporal submission)
- Updated: backend/src/api/runs.py (Temporal status/results)
- Updated: backend/src/main.py (727 lines, TemporalManager integration)
- Updated: All 16 MCP tools to use TemporalManager

## Testing
- ✅ All services healthy (Temporal, PostgreSQL, MinIO, workers, backend)
- ✅ All API endpoints functional
- ✅ End-to-end workflow test passed (72 findings from vulnerable_app)
- ✅ MinIO storage integration working (target upload/download, results)
- ✅ Worker activity discovery working (6 activities registered)
- ✅ Tarball extraction working
- ✅ SARIF report generation working

## Documentation
- ARCHITECTURE.md: Complete Temporal architecture documentation
- QUICKSTART_TEMPORAL.md: Getting started guide
- MIGRATION_DECISION.md: Why we chose Temporal over Prefect
- IMPLEMENTATION_STATUS.md: Migration progress tracking
- workers/README.md: Worker development guide

## Dependencies
- Added: temporalio>=1.6.0
- Added: boto3>=1.34.0 (MinIO S3 client)
- Removed: prefect>=3.4.18

* feat: Add Python fuzzing vertical with Atheris integration

This commit implements a complete Python fuzzing workflow using Atheris:

## Python Worker (workers/python/)
- Dockerfile with Python 3.11, Atheris, and build tools
- Generic worker.py for dynamic workflow discovery
- requirements.txt with temporalio, boto3, atheris dependencies
- Added to docker-compose.temporal.yaml with dedicated cache volume

## AtherisFuzzer Module (backend/toolbox/modules/fuzzer/)
- Reusable module extending BaseModule
- Auto-discovers fuzz targets (fuzz_*.py, *_fuzz.py, fuzz_target.py)
- Recursive search to find targets in nested directories
- Dynamically loads TestOneInput() function
- Configurable max_iterations and timeout
- Real-time stats callback support for live monitoring
- Returns findings as ModuleFinding objects

## Atheris Fuzzing Workflow (backend/toolbox/workflows/atheris_fuzzing/)
- Temporal workflow for orchestrating fuzzing
- Downloads user code from MinIO
- Executes AtherisFuzzer module
- Uploads results to MinIO
- Cleans up cache after execution
- metadata.yaml with vertical: python for routing

## Test Project (test_projects/python_fuzz_waterfall/)
- Demonstrates stateful waterfall vulnerability
- main.py with check_secret() that leaks progress
- fuzz_target.py with Atheris TestOneInput() harness
- Complete README with usage instructions

## Backend Fixes
- Fixed parameter merging in REST API endpoints (workflows.py)
- Changed workflow parameter passing from positional args to kwargs (manager.py)
- Default parameters now properly merged with user parameters

## Testing
✅ Worker discovered AtherisFuzzingWorkflow
✅ Workflow executed end-to-end successfully
✅ Fuzz target auto-discovered in nested directories
✅ Atheris ran 100,000 iterations
✅ Results uploaded and cache cleaned

* chore: Complete Temporal migration with updated CLI/SDK/docs

This commit includes all remaining Temporal migration changes:

## CLI Updates (cli/)
- Updated workflow execution commands for Temporal
- Enhanced error handling and exceptions
- Updated dependencies in uv.lock

## SDK Updates (sdk/)
- Client methods updated for Temporal workflows
- Updated models for new workflow execution
- Updated dependencies in uv.lock

## Documentation Updates (docs/)
- Architecture documentation for Temporal
- Workflow concept documentation
- Resource management documentation (new)
- Debugging guide (new)
- Updated tutorials and how-to guides
- Troubleshooting updates

## README Updates
- Main README with Temporal instructions
- Backend README
- CLI README
- SDK README

## Other
- Updated IMPLEMENTATION_STATUS.md
- Removed old vulnerable_app.tar.gz

These changes complete the Temporal migration and ensure the
CLI/SDK work correctly with the new backend.

* fix: Use positional args instead of kwargs for Temporal workflows

The Temporal Python SDK's start_workflow() method doesn't accept
a 'kwargs' parameter. Workflows must receive parameters as positional
arguments via the 'args' parameter.

Changed from:
  args=workflow_args  # Positional arguments

This fixes the error:
  TypeError: Client.start_workflow() got an unexpected keyword argument 'kwargs'

Workflows now correctly receive parameters in order:
- security_assessment: [target_id, scanner_config, analyzer_config, reporter_config]
- atheris_fuzzing: [target_id, target_file, max_iterations, timeout_seconds]
- rust_test: [target_id, test_message]

* fix: Filter metadata-only parameters from workflow arguments

SecurityAssessmentWorkflow was receiving 7 arguments instead of 2-5.
The issue was that target_path and volume_mode from default_parameters
were being passed to the workflow, when they should only be used by
the system for configuration.

Now filters out metadata-only parameters (target_path, volume_mode)
before passing arguments to workflow execution.

* refactor: Remove Prefect leftovers and volume mounting legacy

Complete cleanup of Prefect migration artifacts:

Backend:
- Delete registry.py and workflow_discovery.py (Prefect-specific files)
- Remove Docker validation from setup.py (no longer needed)
- Remove ResourceLimits and VolumeMount models
- Remove target_path and volume_mode from WorkflowSubmission
- Remove supported_volume_modes from API and discovery
- Clean up metadata.yaml files (remove volume/path fields)
- Simplify parameter filtering in manager.py

SDK:
- Remove volume_mode parameter from client methods
- Remove ResourceLimits and VolumeMount models
- Remove Prefect error patterns from docker_logs.py
- Clean up WorkflowSubmission and WorkflowMetadata models

CLI:
- Remove Volume Modes display from workflow info

All removed features are Prefect-specific or Docker volume mounting
artifacts. Temporal workflows use MinIO storage exclusively.

* feat: Add comprehensive test suite and benchmark infrastructure

- Add 68 unit tests for fuzzer, scanner, and analyzer modules
- Implement pytest-based test infrastructure with fixtures
- Add 6 performance benchmarks with category-specific thresholds
- Configure GitHub Actions for automated testing and benchmarking
- Add test and benchmark documentation

Test coverage:
- AtherisFuzzer: 8 tests
- CargoFuzzer: 14 tests
- FileScanner: 22 tests
- SecurityAnalyzer: 24 tests

All tests passing (68/68)
All benchmarks passing (6/6)

* fix: Resolve all ruff linting violations across codebase

Fixed 27 ruff violations in 12 files:
- Removed unused imports (Depends, Dict, Any, Optional, etc.)
- Fixed undefined workflow_info variable in workflows.py
- Removed dead code with undefined variables in atheris_fuzzer.py
- Changed f-string to regular string where no placeholders used

All files now pass ruff checks for CI/CD compliance.

* fix: Configure CI for unit tests only

- Renamed docker-compose.temporal.yaml → docker-compose.yml for CI compatibility
- Commented out integration-tests job (no integration tests yet)
- Updated test-summary to only depend on lint and unit-tests

CI will now run successfully with 68 unit tests. Integration tests can be added later.

* feat: Add CI/CD integration with ephemeral deployment model

Implements comprehensive CI/CD support for FuzzForge with on-demand worker management:

**Worker Management (v0.7.0)**
- Add WorkerManager for automatic worker lifecycle control
- Auto-start workers from stopped state when workflows execute
- Auto-stop workers after workflow completion
- Health checks and startup timeout handling (90s default)

**CI/CD Features**
- `--fail-on` flag: Fail builds based on SARIF severity levels (error/warning/note/info)
- `--export-sarif` flag: Export findings in SARIF 2.1.0 format
- `--auto-start`/`--auto-stop` flags: Control worker lifecycle
- Exit code propagation: Returns 1 on blocking findings, 0 on success

**Exit Code Fix**
- Add `except typer.Exit: raise` handlers at 3 critical locations
- Move worker cleanup to finally block for guaranteed execution
- Exit codes now propagate correctly even when build fails

**CI Scripts & Examples**
- ci-start.sh: Start FuzzForge services with health checks
- ci-stop.sh: Clean shutdown with volume preservation option
- GitHub Actions workflow example (security-scan.yml)
- GitLab CI pipeline example (.gitlab-ci.example.yml)
- docker-compose.ci.yml: CI-optimized compose file with profiles

**OSS-Fuzz Integration**
- New ossfuzz_campaign workflow for running OSS-Fuzz projects
- OSS-Fuzz worker with Docker-in-Docker support
- Configurable campaign duration and project selection

**Documentation**
- Comprehensive CI/CD integration guide (docs/how-to/cicd-integration.md)
- Updated architecture docs with worker lifecycle details
- Updated workspace isolation documentation
- CLI README with worker management examples

**SDK Enhancements**
- Add get_workflow_worker_info() endpoint
- Worker vertical metadata in workflow responses

**Testing**
- All workflows tested: security_assessment, atheris_fuzzing, secret_detection, cargo_fuzzing
- All monitoring commands tested: stats, crashes, status, finding
- Full CI pipeline simulation verified
- Exit codes verified for success/failure scenarios

Ephemeral CI/CD model: ~3-4GB RAM, ~60-90s startup, runs entirely in CI containers.

* fix: Resolve ruff linting violations in CI/CD code

- Remove unused variables (run_id, defaults, result)
- Remove unused imports
- Fix f-string without placeholders

All CI/CD integration files now pass ruff checks.

test_security_workflow.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python3
+"""
+Test security_assessment workflow with vulnerable_app test project
+"""
+
+import asyncio
+import shutil
+import sys
+import uuid
+from pathlib import Path
+
+import boto3
+from temporalio.client import Client
+
+
+async def main():
+    # Configuration
+    temporal_address = "localhost:7233"
+    s3_endpoint = "http://localhost:9000"
+    s3_access_key = "fuzzforge"
+    s3_secret_key = "fuzzforge123"
+
+    # Initialize S3 client
+    s3_client = boto3.client(
+        's3',
+        endpoint_url=s3_endpoint,
+        aws_access_key_id=s3_access_key,
+        aws_secret_access_key=s3_secret_key,
+        region_name='us-east-1',
+        use_ssl=False
+    )
+
+    print("=" * 70)
+    print("Testing security_assessment workflow with vulnerable_app")
+    print("=" * 70)
+
+    # Step 1: Create tarball of vulnerable_app
+    print("\n[1/5] Creating tarball of test_projects/vulnerable_app...")
+    vulnerable_app_dir = Path("test_projects/vulnerable_app")
+
+    if not vulnerable_app_dir.exists():
+        print(f"❌ Error: {vulnerable_app_dir} not found")
+        return 1
+
+    target_id = str(uuid.uuid4())
+    tarball_path = f"/tmp/{target_id}.tar.gz"
+
+    # Create tarball
+    shutil.make_archive(
+        tarball_path.replace('.tar.gz', ''),
+        'gztar',
+        root_dir=vulnerable_app_dir.parent,
+        base_dir=vulnerable_app_dir.name
+    )
+
+    tarball_size = Path(tarball_path).stat().st_size
+    print(f"✓ Created tarball: {tarball_path} ({tarball_size / 1024:.2f} KB)")
+
+    # Step 2: Upload to MinIO
+    print(f"\n[2/5] Uploading target to MinIO (target_id={target_id})...")
+    try:
+        s3_key = f'{target_id}/target'
+        s3_client.upload_file(
+            Filename=tarball_path,
+            Bucket='targets',
+            Key=s3_key
+        )
+        print(f"✓ Uploaded to s3://targets/{s3_key}")
+    except Exception as e:
+        print(f"❌ Failed to upload: {e}")
+        return 1
+    finally:
+        # Cleanup local tarball
+        Path(tarball_path).unlink(missing_ok=True)
+
+    # Step 3: Connect to Temporal
+    print(f"\n[3/5] Connecting to Temporal at {temporal_address}...")
+    try:
+        client = await Client.connect(temporal_address)
+        print("✓ Connected to Temporal")
+    except Exception as e:
+        print(f"❌ Failed to connect to Temporal: {e}")
+        return 1
+
+    # Step 4: Execute workflow
+    print("\n[4/5] Executing security_assessment workflow...")
+    workflow_id = f"security-assessment-{target_id}"
+
+    try:
+        result = await client.execute_workflow(
+            "SecurityAssessmentWorkflow",
+            args=[target_id],
+            id=workflow_id,
+            task_queue="rust-queue"
+        )
+
+        print(f"✓ Workflow completed successfully: {workflow_id}")
+
+    except Exception as e:
+        print(f"❌ Workflow execution failed: {e}")
+        return 1
+
+    # Step 5: Display results
+    print("\n[5/5] Results Summary:")
+    print("=" * 70)
+
+    if result.get("status") == "success":
+        summary = result.get("summary", {})
+        print(f"Total findings: {summary.get('total_findings', 0)}")
+        print(f"Files scanned: {summary.get('files_scanned', 0)}")
+
+        # Display SARIF results URL if available
+        if result.get("results_url"):
+            print(f"Results URL: {result['results_url']}")
+
+        # Show workflow steps
+        print("\nWorkflow steps:")
+        for step in result.get("steps", []):
+            status_icon = "✓" if step["status"] == "success" else "✗"
+            print(f"  {status_icon} {step['step']}")
+
+        print("\n" + "=" * 70)
+        print("✅ Security assessment workflow test PASSED")
+        print("=" * 70)
+        return 0
+    else:
+        print(f"❌ Workflow failed: {result.get('error', 'Unknown error')}")
+        return 1
+
+
+if __name__ == "__main__":
+    try:
+        exit_code = asyncio.run(main())
+        sys.exit(exit_code)
+    except KeyboardInterrupt:
+        print("\n\nTest interrupted by user")
+        sys.exit(1)
+    except Exception as e:
+        print(f"\n❌ Fatal error: {e}")
+        import traceback
+        traceback.print_exc()
+        sys.exit(1)