Add support for headless Ghidra and stdio MCP server

- Add pyghidra support
- Add manual MCP server start
- Add python package again
- Add end to end tests
- Test in docker container

Author: claude

.github/CI_WORKFLOWS.md

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+# GitHub Actions CI Workflows
+
+This document describes the CI/CD workflows for the ReVa project.
+
+## Workflows Overview
+
+### 1. `test-ghidra.yml` - Main Extension Tests
+
+**Triggers**: Push/PR to main or develop branches
+
+**What it does**:
+- Tests ReVa as a Ghidra extension (GUI mode)
+- Runs unit tests and integration tests
+- Tests on multiple Ghidra versions (11.4, 11.4.2, latest)
+- Includes lint checks and CodeQL security analysis
+
+**Jobs**:
+- `test` - Runs gradle unit and integration tests
+- `lint` - Code compilation checks
+- `codeql` - Security vulnerability scanning
+
+**Duration**: ~10-15 minutes per matrix job
+
+### 2. `test-headless.yml` - Headless Mode Tests
+
+**Triggers**:
+- Push/PR to main or develop (when headless files change)
+- Manual workflow dispatch
+
+**What it does**:
+- Tests ReVa in headless Ghidra mode via pyghidra
+- Runs Python-based headless server tests
+- Tests on multiple OS (Ubuntu, macOS, Windows)
+- Tests on multiple Ghidra versions (11.4.2, latest)
+- Tests on multiple Python versions (3.9, 3.11, 3.12)
+
+**Jobs**:
+- `test-headless` - Unix/Mac matrix testing
+- `test-headless-windows` - Windows-specific testing
+- `test-summary` - Aggregates results
+
+**Duration**: ~5-8 minutes per matrix job
+
+**Test Coverage**:
+1. Quick smoke test (start/stop/verify)
+2. Custom port configuration
+3. Configuration file loading
+4. Cross-platform compatibility
+
+### 3. `publish-ghidra.yml` - Release Publishing
+
+**Triggers**: Manual or release tags
+
+**What it does**:
+- Builds and publishes release artifacts
+- Creates GitHub releases
+- Uploads extension zip files
+
+**Duration**: ~5 minutes
+
+### 4. `claude.yml` - Claude Code Integration
+
+**Triggers**: Varies (project-specific)
+
+**What it does**:
+- Claude Code specific automation
+- May include code review, documentation, etc.
+
+## Test Matrix Strategy
+
+### Main Extension Tests (`test-ghidra.yml`)
+
+```
+Matrix:
+  OS: ubuntu-latest
+  Ghidra: [11.4, 11.4.2, latest]
+
+Total: 3 jobs
+```
+
+### Headless Mode Tests (`test-headless.yml`)
+
+```
+Unix/Mac Matrix:
+  OS: [ubuntu-latest, macos-latest]
+  Ghidra: [11.4.2, latest]
+  Python: [3.9, 3.11, 3.12]
+  Excludes: (11.4.2 + older Python versions)
+
+  Total: 8 jobs (2 OS × 2 Ghidra × 2 Python combinations)
+
+Windows:
+  OS: windows-latest
+  Ghidra: latest
+  Python: 3.12
+
+  Total: 1 job
+
+Grand Total: 9 jobs
+```
+
+## Workflow Optimization
+
+### Path Filtering
+
+The headless workflow only runs when relevant files change:
+- `src/main/java/reva/headless/**`
+- `src/main/java/reva/plugin/config/**`
+- `scripts/**`
+- `config/**`
+- Configuration files
+
+This reduces unnecessary CI runs when unrelated files change.
+
+### Matrix Exclusions
+
+The headless workflow excludes some combinations to reduce CI time:
+- Only tests older Python versions (3.9, 3.11) on latest Ghidra
+- Tests Python 3.12 on all Ghidra versions
+- Balances coverage vs. execution time
+
+### Fail-Fast: Disabled
+
+Both test workflows use `fail-fast: false` to ensure all matrix jobs complete even if some fail. This provides complete test coverage visibility.
+
+## Running Workflows
+
+### Automatic Triggers
+
+Both workflows automatically run on:
+- Push to `main` or `develop` branches
+- Pull requests to `main` or `develop` branches
+
+### Manual Triggers
+
+The headless workflow can be manually triggered:
+
+1. Go to Actions tab in GitHub
+2. Select "Test Headless Mode 🤖"
+3. Click "Run workflow"
+4. Select branch
+5. Click "Run workflow"
+
+This is useful for:
+- Testing on feature branches
+- Debugging CI issues
+- Validating fixes
+
+## Debugging Failed Tests
+
+### View Test Results
+
+1. Click on failed workflow run
+2. Click on failed job
+3. Expand failing step to see logs
+
+### Download Artifacts
+
+Failed runs upload artifacts:
+- Test results (XML/HTML)
+- Log files
+- Configuration files
+
+Download via workflow run page → Artifacts section
+
+### Common Issues
+
+**Issue: PyGhidra import fails**
+```
+ImportError: No module named 'pyghidra'
+```
+**Solution**: Check pip install step completed successfully
+
+**Issue: Ghidra not found**
+```
+GHIDRA_INSTALL_DIR not set
+```
+**Solution**: Check setup-ghidra action completed successfully
+
+**Issue: Timeout**
+```
+Error: The operation was canceled.
+```
+**Solution**: Increase timeout or check for hanging processes
+
+**Issue: Port already in use**
+```
+BindException: Address already in use
+```
+**Solution**: Tests should use different ports or proper cleanup
+
+## Performance Benchmarks
+
+### Expected Durations
+
+| Workflow | Jobs | Avg Time/Job | Total Time (parallel) |
+|----------|------|--------------|----------------------|
+| test-ghidra.yml | 3 + lint + codeql | 12 min | ~15 min |
+| test-headless.yml | 9 | 6 min | ~8 min |
+| publish-ghidra.yml | 1 | 5 min | ~5 min |
+
+### Parallelization
+
+Both test workflows run matrix jobs in parallel, significantly reducing total CI time compared to sequential execution.
+
+## CI/CD Best Practices
+
+### For Contributors
+
+1. **Run tests locally first** when possible
+   ```bash
+   # Main tests
+   gradle test
+   gradle integrationTest
+
+   # Headless tests
+   python scripts/test_headless_quick.py
+   ```
+
+2. **Use draft PRs** for work in progress to avoid unnecessary CI runs
+
+3. **Path filtering** means not all changes trigger all workflows
+
+4. **Check CI status** before requesting review
+
+### For Maintainers
+
+1. **Review test results** before merging PRs
+
+2. **Monitor CI performance** and adjust matrix if needed
+
+3. **Update workflows** when:
+   - New Ghidra version released
+   - Python version EOL
+   - Dependencies updated
+
+4. **Keep documentation updated** when changing workflows
+
+## Troubleshooting CI
+
+### Workflow doesn't trigger
+
+**Check**:
+- Branch name matches trigger pattern
+- File paths match path filter
+- Workflow file is valid YAML
+
+### Tests pass locally but fail in CI
+
+**Common causes**:
+- Environment differences (OS, versions)
+- Missing dependencies in CI
+- Timeout too short
+- Race conditions
+
+**Debug**:
+1. Check workflow environment matches local
+2. Add debug logging to tests
+3. Increase timeouts
+4. Use workflow dispatch to test manually
+
+### Long CI times
+
+**Optimization options**:
+1. Reduce matrix size
+2. Add path filters
+3. Use caching for dependencies
+4. Increase parallelization
+
+## Monitoring
+
+### Workflow Status Badge
+
+Add to README:
+```markdown
+![Test Headless Mode](https://github.com/your-org/reverse-engineering-assistant/actions/workflows/test-headless.yml/badge.svg)
+```
+
+### Notifications
+
+GitHub sends notifications on:
+- Workflow failures (to committer)
+- Status changes (if watching repo)
+
+Configure in GitHub settings → Notifications
+
+## Future Enhancements
+
+Potential workflow improvements:
+
+1. **Performance Tests**
+   - Benchmark startup times
+   - Memory usage profiling
+   - API response times
+
+2. **E2E Tests**
+   - Full MCP client integration
+   - Real binary analysis
+   - Multi-tool workflows
+
+3. **Docker Tests**
+   - Build Docker image
+   - Test container deployment
+   - Docker Compose orchestration
+
+4. **Coverage Reports**
+   - JaCoCo for Java
+   - Coverage.py for Python
+   - Combined coverage metrics
+
+5. **Automated Releases**
+   - Version bumping
+   - Changelog generation
+   - Asset uploads
+
+## References
+
+- [GitHub Actions Documentation](https://docs.github.com/en/actions)
+- [setup-ghidra Action](https://github.com/antoniovazquezblanco/setup-ghidra)
+- [Gradle Actions](https://github.com/gradle/actions)
+- [PyGhidra Documentation](https://github.com/dod-cyber-crime-center/pyghidra)