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.

cli/src/fuzzforge_cli/main.py

@@ -117,7 +117,6 @@ def config(
     """
     ⚙️  Manage configuration (show all, get, or set values)
     """
-    from .commands import config as config_cmd
 
     if key is None:
         # No arguments: show all config
@@ -205,10 +204,29 @@ def run_workflow(
     live: bool = typer.Option(
         False, "--live", "-l",
         help="Start live monitoring after execution (useful for fuzzing workflows)"
+    ),
+    auto_start: Optional[bool] = typer.Option(
+        None, "--auto-start/--no-auto-start",
+        help="Automatically start required worker if not running (default: from config)"
+    ),
+    auto_stop: Optional[bool] = typer.Option(
+        None, "--auto-stop/--no-auto-stop",
+        help="Automatically stop worker after execution completes (default: from config)"
+    ),
+    fail_on: Optional[str] = typer.Option(
+        None, "--fail-on",
+        help="Fail build if findings match SARIF level (error,warning,note,info,all,none). Use with --wait"
+    ),
+    export_sarif: Optional[str] = typer.Option(
+        None, "--export-sarif",
+        help="Export SARIF results to file after completion. Use with --wait"
     )
 ):
     """
     🚀 Execute a security testing workflow
+
+    Use --fail-on with --wait to fail CI builds based on finding severity.
+    Use --export-sarif with --wait to export SARIF findings to a file.
     """
     from .commands.workflow_exec import execute_workflow
 
@@ -221,7 +239,11 @@ def run_workflow(
         timeout=timeout,
         interactive=interactive,
         wait=wait,
-        live=live
+        live=live,
+        auto_start=auto_start,
+        auto_stop=auto_stop,
+        fail_on=fail_on,
+        export_sarif=export_sarif
     )
 
 @workflow_app.callback()
@@ -356,43 +378,6 @@ app.add_typer(ai.app, name="ai", help="🤖 AI integration features")
 app.add_typer(ingest.app, name="ingest", help="🧠 Ingest knowledge into AI")
 
 # Help and utility commands
-@app.command()
-def examples():
-    """
-    📚 Show usage examples
-    """
-    examples_text = """
-[bold cyan]FuzzForge CLI Examples[/bold cyan]
-
-[bold]Getting Started:[/bold]
-  ff init                           # Initialize a project
-  ff workflows                      # List available workflows
-  ff workflow info afl-fuzzing      # Get workflow details
-
-[bold]Execute Workflows:[/bold]
-  ff workflow afl-fuzzing ./target  # Run fuzzing on target
-  ff workflow afl-fuzzing . --live  # Run with live monitoring
-  ff workflow scan-c ./src timeout=300 threads=4  # With parameters
-
-[bold]Monitor Execution:[/bold]
-  ff status                         # Check latest execution
-  ff workflow status                # Same as above
-  ff monitor                        # Live monitoring dashboard
-  ff workflow history               # Show past executions
-
-[bold]Review Findings:[/bold]
-  ff findings                       # List all findings
-  ff finding                        # Show latest finding
-  ff finding export --format sarif  # Export findings
-
-[bold]AI Features:[/bold]
-  ff ai chat                        # Interactive AI chat
-  ff ai suggest ./src               # Get workflow suggestions
-  ff finding analyze                # AI analysis of latest finding
-"""
-    console.print(examples_text)
-
-
 @app.command()
 def version():
     """
@@ -400,7 +385,7 @@ def version():
     """
     from . import __version__
     console.print(f"FuzzForge CLI v{__version__}")
-    console.print(f"Short command: ff")
+    console.print("Short command: ff")
 
 
 @app.callback()
@@ -418,7 +403,6 @@ def main_callback(
     • ff init                        - Initialize a new project
     • ff workflows                   - See available workflows
     • ff workflow <name> <target>    - Execute a workflow
-    • ff examples                    - Show usage examples
     """
     if version:
         from . import __version__
@@ -468,7 +452,7 @@ def main():
                     'workflows', 'workflow',
                     'findings', 'finding',
                     'monitor', 'ai', 'ingest',
-                    'examples', 'version'
+                    'version'
                 ]
 
                 if main_cmd not in valid_commands: