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/README.md

@@ -153,10 +153,10 @@ fuzzforge workflows parameters security_assessment --no-interactive
 ### Workflow Execution
 
 #### `fuzzforge workflow <workflow> <target-path>`
-Execute a security testing workflow.
+Execute a security testing workflow with **automatic file upload**.
 
 ```bash
-# Basic execution
+# Basic execution - CLI automatically detects local files and uploads them
 fuzzforge workflow security_assessment /path/to/code
 
 # With parameters
@@ -172,6 +172,49 @@ fuzzforge workflow security_assessment /path/to/code \
 fuzzforge workflow security_assessment /path/to/code --wait
 ```
 
+**Automatic File Upload Behavior:**
+
+The CLI intelligently handles target files based on whether they exist locally:
+
+1. **Local file/directory exists** → **Automatic upload to MinIO**:
+   - CLI creates a compressed tarball (`.tar.gz`) for directories
+   - Uploads via HTTP to backend API
+   - Backend stores in MinIO with unique `target_id`
+   - Worker downloads from MinIO when ready to analyze
+   - ✅ **Works from any machine** (no shared filesystem needed)
+
+2. **Path doesn't exist locally** → **Path-based submission** (legacy):
+   - Path is sent to backend as-is
+   - Backend expects target to be accessible on its filesystem
+   - ⚠️ Only works when CLI and backend share filesystem
+
+**Example workflow:**
+```bash
+$ ff workflow security_assessment ./my-project
+
+🔧 Getting workflow information for: security_assessment
+📦 Detected local directory: ./my-project (21 files)
+🗜️  Creating compressed tarball...
+📤 Uploading to backend (0.01 MB)...
+✅ Upload complete! Target ID: 548193a1-f73f-4ec1-8068-19ec2660b8e4
+
+🎯 Executing workflow:
+   Workflow: security_assessment
+   Target: my-project.tar.gz (uploaded)
+   Volume Mode: ro
+   Status: 🔄 RUNNING
+
+✅ Workflow started successfully!
+   Execution ID: security_assessment-52781925
+```
+
+**Upload Details:**
+- **Max file size**: 10 GB (configurable on backend)
+- **Compression**: Automatic for directories (reduces upload time)
+- **Storage**: Files stored in MinIO (S3-compatible)
+- **Lifecycle**: Automatic cleanup after 7 days
+- **Caching**: Workers cache downloaded targets for faster repeated workflows
+
 **Options:**
 - `--param, -p` - Parameter in key=value format (can be used multiple times)
 - `--param-file, -f` - JSON file containing parameters
@@ -181,6 +224,22 @@ fuzzforge workflow security_assessment /path/to/code --wait
 - `--wait, -w` - Wait for execution to complete
 - `--live, -l` - Show live monitoring during execution
 
+**Worker Lifecycle Options (v0.7.0):**
+- `--auto-start/--no-auto-start` - Auto-start required worker (default: from config)
+- `--auto-stop/--no-auto-stop` - Auto-stop worker after completion (default: from config)
+
+**Examples:**
+```bash
+# Worker starts automatically (default behavior)
+fuzzforge workflow ossfuzz_campaign . project_name=zlib
+
+# Disable auto-start (worker must be running already)
+fuzzforge workflow ossfuzz_campaign . --no-auto-start
+
+# Auto-stop worker after completion
+fuzzforge workflow ossfuzz_campaign . --wait --auto-stop
+```
+
 #### `fuzzforge workflow status [execution-id]`
 Check the status of a workflow execution.
 
@@ -402,6 +461,12 @@ preferences:
   show_progress_bars: true
   table_style: "rich"
   color_output: true
+
+workers:
+  auto_start_workers: true    # Auto-start workers when needed
+  auto_stop_workers: false    # Auto-stop workers after completion
+  worker_startup_timeout: 60  # Worker startup timeout (seconds)
+  docker_compose_file: null   # Custom docker-compose.yml path
 ```
 
 ## 🔧 Advanced Usage