From 9583631ffe49fa4652e95f04ba0d20f514f74775 Mon Sep 17 00:00:00 2001
From: Oscar V <oscarvalenzuelab@users.noreply.github.com>
Date: Tue, 4 Nov 2025 17:56:38 -0800
Subject: [PATCH] Add missing documentation files

- Created docs/user-guide.md with comprehensive usage examples
- Created docs/api.md with Python API reference
- Created docs/discovery-methods.md with detailed identification strategies
- Created docs/examples.md with common use cases and workflows

Documentation now matches README references
---
 docs/api.md               | 497 +++++++++++++++++++++++++
 docs/discovery-methods.md | 425 ++++++++++++++++++++++
 docs/examples.md          | 747 ++++++++++++++++++++++++++++++++++++++
 docs/user-guide.md        | 370 +++++++++++++++++++
 4 files changed, 2039 insertions(+)
 create mode 100644 docs/api.md
 create mode 100644 docs/discovery-methods.md
 create mode 100644 docs/examples.md
 create mode 100644 docs/user-guide.md

diff --git a/docs/api.md b/docs/api.md
new file mode 100644
index 0000000..f7f12ca
--- /dev/null
+++ b/docs/api.md
@@ -0,0 +1,497 @@
+# SRC2PURL API Reference
+
+Complete API documentation for the SRC2PURL Python library.
+
+## Core Functions
+
+### `identify_package()`
+
+Main function for identifying packages from source code.
+
+```python
+identify_package(
+    path: str,
+    use_swh: bool = False,
+    confidence_threshold: float = 0.3,
+    detect_subcomponents: bool = False,
+    max_depth: int = 2,
+    no_license_detection: bool = False,
+    verbose: bool = False,
+    no_cache: bool = False,
+    api_token: str = None
+) -> PackageIdentification
+```
+
+#### Parameters
+
+- **path** (str): Path to source code directory to analyze
+- **use_swh** (bool): Enable Software Heritage archive checking (default: False)
+- **confidence_threshold** (float): Minimum confidence score (0.0-1.0, default: 0.3)
+- **detect_subcomponents** (bool): Detect components in monorepos (default: False)
+- **max_depth** (int): Maximum directory traversal depth (default: 2)
+- **no_license_detection** (bool): Skip license detection (default: False)
+- **verbose** (bool): Enable verbose output (default: False)
+- **no_cache** (bool): Disable caching (default: False)
+- **api_token** (str): Software Heritage API token (default: None)
+
+#### Returns
+
+`PackageIdentification` object with package information.
+
+#### Example
+
+```python
+from src2purl import identify_package
+
+result = identify_package(
+    "/path/to/project",
+    confidence_threshold=0.85,
+    verbose=True
+)
+
+print(f"Found: {result.name}@{result.version}")
+```
+
+## Data Classes
+
+### `PackageIdentification`
+
+Result object containing package identification information.
+
+#### Attributes
+
+- **name** (str): Package name
+- **version** (str): Package version
+- **purl** (str): Package URL (PURL)
+- **license** (str): Detected license
+- **confidence** (float): Confidence score (0.0-1.0)
+- **ecosystem** (str): Package ecosystem (npm, pypi, maven, etc.)
+- **description** (str): Package description
+- **homepage** (str): Project homepage URL
+- **repository_url** (str): Source repository URL
+- **discovery_methods** (List[str]): Methods used for discovery
+- **subcomponents** (List[PackageIdentification]): Detected subcomponents
+- **metadata** (dict): Additional metadata
+
+#### Methods
+
+```python
+# Convert to dictionary
+result.to_dict() -> dict
+
+# Convert to JSON
+result.to_json() -> str
+
+# Check if valid
+result.is_valid() -> bool
+
+# Get PURL object
+result.get_purl() -> PackageURL
+```
+
+### `PackageURL`
+
+PURL (Package URL) representation.
+
+```python
+from packageurl import PackageURL
+
+purl = PackageURL(
+    type='npm',
+    namespace='@angular',
+    name='core',
+    version='12.0.0'
+)
+
+print(purl.to_string())
+# pkg:npm/@angular/core@12.0.0
+```
+
+## Discovery Classes
+
+### `HashBasedDiscovery`
+
+Performs hash-based package discovery using SWHID.
+
+```python
+from src2purl.discovery import HashBasedDiscovery
+
+discovery = HashBasedDiscovery()
+result = discovery.identify(
+    directory_path="/path/to/source",
+    use_swh=False
+)
+```
+
+### `ManifestDiscovery`
+
+Extracts package information from manifest files.
+
+```python
+from src2purl.discovery import ManifestDiscovery
+
+discovery = ManifestDiscovery()
+result = discovery.extract_from_manifests("/path/to/source")
+```
+
+## Utility Functions
+
+### `validate_swhid()`
+
+Validate Software Heritage ID for a directory.
+
+```python
+from src2purl.utils import validate_swhid
+
+swhid = validate_swhid(
+    directory_path="/path/to/source",
+    expected_swhid="swh:1:dir:abc123..."
+)
+print(f"Valid: {swhid.is_valid}")
+```
+
+### `clear_cache()`
+
+Clear all cached API responses.
+
+```python
+from src2purl.cache import clear_cache
+
+clear_cache()
+print("Cache cleared")
+```
+
+### `get_cache_stats()`
+
+Get cache usage statistics.
+
+```python
+from src2purl.cache import get_cache_stats
+
+stats = get_cache_stats()
+print(f"Cache size: {stats['size_mb']} MB")
+print(f"Cache entries: {stats['entries']}")
+```
+
+## Configuration
+
+### Environment Variables
+
+Configure SRC2PURL using environment variables:
+
+```python
+import os
+
+# Set API tokens from environment
+os.environ['GITHUB_TOKEN'] = os.getenv('GITHUB_TOKEN')
+os.environ['SCANOSS_API_KEY'] = os.getenv('SCANOSS_API_KEY')
+os.environ['SWH_API_TOKEN'] = os.getenv('SWH_API_TOKEN')
+
+# Set cache directory
+os.environ['SRC2PURL_CACHE_DIR'] = '/custom/cache/path'
+
+# Set default max depth
+os.environ['SRC2PURL_MAX_DEPTH'] = '3'
+```
+
+### Configuration Object
+
+```python
+from src2purl.config import Config
+
+config = Config(
+    cache_dir="~/.cache/src2purl",
+    max_depth=2,
+    default_confidence_threshold=0.3,
+    github_token=os.getenv('GITHUB_TOKEN'),
+    scanoss_api_key=os.getenv('SCANOSS_API_KEY'),
+    swh_api_token=os.getenv('SWH_API_TOKEN')
+)
+
+# Apply configuration
+config.apply()
+```
+
+## Advanced Usage
+
+### Custom Discovery Pipeline
+
+```python
+from src2purl import identify_package
+from src2purl.discovery import DiscoveryPipeline
+
+# Create custom pipeline
+pipeline = DiscoveryPipeline()
+pipeline.add_stage(HashBasedDiscovery())
+pipeline.add_stage(ManifestDiscovery())
+pipeline.add_stage(LicenseDiscovery())
+
+# Run pipeline
+result = pipeline.run("/path/to/source")
+```
+
+### Batch Processing with Parallelism
+
+```python
+from src2purl import identify_package
+from concurrent.futures import ThreadPoolExecutor
+import json
+
+def process_project(path):
+    try:
+        result = identify_package(path)
+        return {
+            'path': path,
+            'purl': result.purl,
+            'confidence': result.confidence,
+            'success': True
+        }
+    except Exception as e:
+        return {
+            'path': path,
+            'error': str(e),
+            'success': False
+        }
+
+# Process multiple projects in parallel
+projects = [
+    '/path/to/project1',
+    '/path/to/project2',
+    '/path/to/project3'
+]
+
+with ThreadPoolExecutor(max_workers=4) as executor:
+    results = list(executor.map(process_project, projects))
+
+# Save results
+with open('batch_results.json', 'w') as f:
+    json.dump(results, f, indent=2)
+```
+
+### Custom Confidence Scoring
+
+```python
+from src2purl import identify_package
+
+def custom_confidence_scorer(result):
+    """Custom confidence scoring logic"""
+    score = result.confidence
+
+    # Boost confidence for certain ecosystems
+    if result.ecosystem == 'npm':
+        score *= 1.1
+
+    # Reduce confidence for old versions
+    if result.version and result.version.startswith('0.'):
+        score *= 0.9
+
+    return min(score, 1.0)
+
+result = identify_package("/path/to/source")
+custom_confidence = custom_confidence_scorer(result)
+print(f"Custom confidence: {custom_confidence:.0%}")
+```
+
+### Integration with SEMCL.ONE Ecosystem
+
+```python
+from src2purl import identify_package
+from purl2src import get_source_url
+from osslili import detect_licenses
+
+# Identify package
+package = identify_package("/path/to/source")
+
+# Get source download URL
+source_url = get_source_url(package.purl)
+
+# Detect licenses
+licenses = detect_licenses("/path/to/source")
+
+# Combine results
+compliance_report = {
+    'package': package.to_dict(),
+    'source_url': source_url,
+    'licenses': licenses
+}
+```
+
+## Error Handling
+
+### Exception Types
+
+```python
+from src2purl.exceptions import (
+    Src2PurlException,
+    DiscoveryException,
+    ValidationException,
+    APIException
+)
+
+try:
+    result = identify_package("/path/to/source")
+except DiscoveryException as e:
+    print(f"Discovery failed: {e}")
+except APIException as e:
+    print(f"API error: {e}")
+except Src2PurlException as e:
+    print(f"General error: {e}")
+```
+
+### Error Recovery
+
+```python
+from src2purl import identify_package
+import logging
+
+logging.basicConfig(level=logging.INFO)
+
+def safe_identify(path, fallback_methods=True):
+    """Identify with fallback strategies"""
+    try:
+        # Try with full features
+        return identify_package(path, use_swh=True)
+    except Exception as e:
+        logging.warning(f"Full identification failed: {e}")
+
+        if fallback_methods:
+            try:
+                # Fallback to fast mode
+                return identify_package(path, use_swh=False)
+            except Exception as e2:
+                logging.error(f"Fallback also failed: {e2}")
+                # Return minimal result
+                return PackageIdentification(
+                    name="unknown",
+                    confidence=0.0
+                )
+```
+
+## Logging
+
+### Configure Logging
+
+```python
+import logging
+from src2purl import identify_package
+
+# Set up logging
+logging.basicConfig(
+    level=logging.DEBUG,
+    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s',
+    handlers=[
+        logging.FileHandler('src2purl.log'),
+        logging.StreamHandler()
+    ]
+)
+
+# Will now produce detailed logs
+result = identify_package("/path/to/source", verbose=True)
+```
+
+### Custom Logger
+
+```python
+import logging
+from src2purl import identify_package
+
+# Create custom logger
+logger = logging.getLogger('src2purl.custom')
+logger.setLevel(logging.INFO)
+
+# Custom handler
+handler = logging.StreamHandler()
+formatter = logging.Formatter('%(message)s')
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+
+# Use with library
+result = identify_package(
+    "/path/to/source",
+    logger=logger
+)
+```
+
+## Testing
+
+### Unit Testing
+
+```python
+import unittest
+from src2purl import identify_package
+from unittest.mock import patch, MagicMock
+
+class TestSrc2Purl(unittest.TestCase):
+    @patch('src2purl.api.github.search_repository')
+    def test_identify_package(self, mock_search):
+        # Mock API response
+        mock_search.return_value = {
+            'name': 'test-package',
+            'version': '1.0.0'
+        }
+
+        result = identify_package('/path/to/test')
+
+        self.assertEqual(result.name, 'test-package')
+        self.assertEqual(result.version, '1.0.0')
+        mock_search.assert_called_once()
+```
+
+### Integration Testing
+
+```python
+import tempfile
+import json
+from pathlib import Path
+from src2purl import identify_package
+
+def test_integration():
+    # Create test project
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Create package.json
+        package_json = Path(tmpdir) / 'package.json'
+        package_json.write_text(json.dumps({
+            'name': 'test-project',
+            'version': '1.0.0',
+            'license': 'MIT'
+        }))
+
+        # Test identification
+        result = identify_package(tmpdir)
+
+        assert result.name == 'test-project'
+        assert result.version == '1.0.0'
+        assert result.ecosystem == 'npm'
+```
+
+## Performance Profiling
+
+```python
+import cProfile
+import pstats
+from src2purl import identify_package
+
+# Profile the identification
+profiler = cProfile.Profile()
+profiler.enable()
+
+result = identify_package("/path/to/large/project")
+
+profiler.disable()
+
+# Print stats
+stats = pstats.Stats(profiler)
+stats.sort_stats('cumulative')
+stats.print_stats(10)  # Top 10 time consumers
+```
+
+## Deprecation Notices
+
+### Deprecated in v2.0
+
+- `identify_from_hash()` - Use `identify_package()` instead
+- `--json-output` flag - Use `--output-format json` instead
+
+### Future Deprecations
+
+- `--api-token` CLI flag - Use environment variables instead
\ No newline at end of file
diff --git a/docs/discovery-methods.md b/docs/discovery-methods.md
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--- /dev/null
+++ b/docs/discovery-methods.md
@@ -0,0 +1,425 @@
+# SRC2PURL Discovery Methods
+
+This document provides a detailed explanation of the identification strategies used by SRC2PURL to discover package coordinates from source code.
+
+## Overview
+
+SRC2PURL employs a sophisticated 2-phase discovery strategy that combines multiple techniques to accurately identify packages from source code directories. The system is designed to be fast (5-15 seconds typical) while maintaining high accuracy.
+
+## Discovery Architecture
+
+```
+Source Directory → Phase 1: Hash-based Discovery → Phase 2: Manifest Enhancement → Result
+                     ├── SWHID Generation           ├── UPMEX Integration
+                     ├── Repository Search          ├── Cross-validation
+                     └── SWH Archive (optional)     └── Metadata Enrichment
+```
+
+## Phase 1: Hash-based Discovery
+
+### 1.1 SWHID Generation
+
+Software Heritage Identifier (SWHID) is a cryptographic hash that uniquely identifies source code directories.
+
+#### How it works:
+
+1. **Directory Traversal**: Recursively processes all files in the directory
+2. **Content Hashing**: Computes Git-compatible hashes for each file
+3. **Merkle Tree**: Builds a tree structure with directory hashes
+4. **SWHID Format**: Produces identifier like `swh:1:dir:94a9ed024d3859793618152ea559a168bbcbb5e2`
+
+#### Implementation:
+
+```python
+def compute_swhid(directory_path):
+    """Compute Software Heritage ID for a directory"""
+    entries = []
+
+    for entry in sorted(os.listdir(directory_path)):
+        path = os.path.join(directory_path, entry)
+
+        if os.path.isfile(path):
+            # Hash file content
+            file_hash = hash_file_git_like(path)
+            entries.append(('file', entry, file_hash))
+        elif os.path.isdir(path):
+            # Recursively hash subdirectory
+            dir_hash = compute_swhid(path)
+            entries.append(('dir', entry, dir_hash))
+
+    # Combine into directory hash
+    return compute_directory_hash(entries)
+```
+
+### 1.2 GitHub Repository Search
+
+Uses the GitHub API to find repositories matching the SWHID.
+
+#### Search Strategy:
+
+1. **File-based Search**: Searches for unique file combinations
+2. **Content Matching**: Matches file contents against GitHub's index
+3. **Repository Metadata**: Extracts package information from found repositories
+
+#### API Usage:
+
+```python
+# Search by file content
+GET https://api.github.com/search/code?q=hash:SWHID
+
+# Get repository details
+GET https://api.github.com/repos/{owner}/{repo}
+
+# Extract package metadata
+GET https://api.github.com/repos/{owner}/{repo}/contents/package.json
+```
+
+#### Rate Limits:
+
+- Without token: 10 requests/hour
+- With token: 5000 requests/hour
+
+### 1.3 SCANOSS Knowledge Base
+
+SCANOSS maintains a comprehensive database of open-source code fingerprints.
+
+#### Process:
+
+1. **Fingerprinting**: Creates WFP (Winnowing Fingerprints) from source files
+2. **API Query**: Sends fingerprints to SCANOSS API
+3. **Match Analysis**: Processes returned component matches
+4. **Confidence Scoring**: Evaluates match quality
+
+#### Fingerprint Generation:
+
+```python
+def generate_wfp(file_content):
+    """Generate Winnowing Fingerprint"""
+    # Create k-grams
+    kgrams = create_kgrams(file_content, k=50)
+
+    # Apply winnowing algorithm
+    fingerprints = winnowing(kgrams, window_size=64)
+
+    # Format as WFP
+    return format_wfp(fingerprints)
+```
+
+### 1.4 Software Heritage Archive (Optional)
+
+When `--use-swh` is enabled, queries the Software Heritage universal source code archive.
+
+#### Capabilities:
+
+- **Comprehensive Coverage**: 190+ million unique source files
+- **Historical Versions**: All versions ever published
+- **Provenance Tracking**: Complete development history
+
+#### Query Process:
+
+```python
+# Check if SWHID exists
+GET https://archive.softwareheritage.org/api/1/directory/{swhid}/
+
+# Get known occurrences
+GET https://archive.softwareheritage.org/api/1/directory/{swhid}/occurrences/
+
+# Extract metadata
+GET https://archive.softwareheritage.org/api/1/origin/{origin_url}/metadata/
+```
+
+#### Performance Impact:
+
+- Adds 60-90+ seconds to processing time
+- Requires rate limit management (60-second delays without token)
+
+## Phase 2: UPMEX Manifest Enhancement
+
+### 2.1 Manifest File Detection
+
+Identifies and parses package manifest files across ecosystems.
+
+#### Supported Manifests:
+
+| Ecosystem | Manifest Files | Metadata Extracted |
+|-----------|---------------|-------------------|
+| NPM/Node.js | package.json, package-lock.json | name, version, license, dependencies |
+| Python | setup.py, pyproject.toml, requirements.txt | name, version, license, classifiers |
+| Java/Maven | pom.xml, build.gradle | groupId, artifactId, version |
+| Ruby | Gemfile, *.gemspec | name, version, license |
+| Go | go.mod, go.sum | module, version, dependencies |
+| Rust | Cargo.toml, Cargo.lock | name, version, license |
+| .NET | *.csproj, packages.config | package ID, version, license |
+| PHP | composer.json, composer.lock | name, version, license |
+
+### 2.2 Manifest Parsing
+
+#### Example: NPM package.json
+
+```python
+def parse_package_json(file_path):
+    """Parse NPM package.json"""
+    with open(file_path) as f:
+        data = json.load(f)
+
+    return {
+        'name': data.get('name'),
+        'version': data.get('version'),
+        'license': normalize_license(data.get('license')),
+        'description': data.get('description'),
+        'repository': extract_repository_url(data.get('repository')),
+        'dependencies': data.get('dependencies', {}),
+        'ecosystem': 'npm'
+    }
+```
+
+#### Example: Python setup.py
+
+```python
+def parse_setup_py(file_path):
+    """Parse Python setup.py using AST"""
+    with open(file_path) as f:
+        tree = ast.parse(f.read())
+
+    # Find setup() call
+    for node in ast.walk(tree):
+        if isinstance(node, ast.Call):
+            if hasattr(node.func, 'id') and node.func.id == 'setup':
+                return extract_setup_kwargs(node)
+```
+
+### 2.3 Cross-validation
+
+Validates Phase 1 findings against manifest data.
+
+#### Validation Rules:
+
+1. **Name Matching**: Package name from manifest vs. repository
+2. **Version Compatibility**: Manifest version vs. tags/releases
+3. **License Agreement**: Detected license vs. declared license
+4. **Dependency Check**: Validate against known dependencies
+
+#### Confidence Scoring:
+
+```python
+def calculate_confidence(phase1_result, phase2_result):
+    """Calculate match confidence"""
+    score = 0.5  # Base score
+
+    # Name match
+    if phase1_result.name == phase2_result.name:
+        score += 0.2
+
+    # Version match
+    if versions_compatible(phase1_result.version, phase2_result.version):
+        score += 0.15
+
+    # License match
+    if phase1_result.license == phase2_result.license:
+        score += 0.1
+
+    # Repository URL match
+    if urls_match(phase1_result.repo_url, phase2_result.repo_url):
+        score += 0.05
+
+    return min(score, 1.0)
+```
+
+## Advanced Discovery Techniques
+
+### 3.1 Monorepo Detection
+
+Identifies multiple packages within a single repository.
+
+#### Detection Strategy:
+
+1. **Pattern Recognition**: Looks for common monorepo structures
+   - `packages/*/package.json` (Lerna/Yarn workspaces)
+   - `apps/*/` and `libs/*/` (Nx)
+   - Multiple `Cargo.toml` files (Rust workspaces)
+
+2. **Workspace Analysis**: Parses workspace configuration files
+
+3. **Independent Scoring**: Each component scored separately
+
+### 3.2 License Detection Enhancement
+
+Uses osslili integration for comprehensive license detection.
+
+#### Process:
+
+1. **Text Analysis**: Scans LICENSE, COPYING, README files
+2. **Header Detection**: Extracts license headers from source files
+3. **SPDX Matching**: Maps to standard SPDX identifiers
+4. **Confidence Weighting**: Weights by file importance
+
+### 3.3 Fuzzy Matching
+
+Handles variations in package identification.
+
+#### Techniques:
+
+1. **Name Normalization**:
+   - Remove special characters
+   - Handle case variations
+   - Account for common prefixes/suffixes
+
+2. **Version Flexibility**:
+   - Semantic version parsing
+   - Range compatibility checking
+   - Git commit hash mapping
+
+3. **Typo Tolerance**:
+   - Levenshtein distance calculation
+   - Common typo patterns
+   - Phonetic matching
+
+## Discovery Method Selection
+
+### Decision Tree:
+
+```
+Start
+  ├── Is it a Git repository?
+  │   └── Yes → Use Git history + GitHub API
+  │   └── No → Continue
+  ├── Has package manifests?
+  │   └── Yes → Parse manifests first
+  │   └── No → Continue
+  ├── Has unique file patterns?
+  │   └── Yes → Use SCANOSS fingerprinting
+  │   └── No → Continue
+  └── Use SWHID + comprehensive search
+```
+
+### Performance vs. Accuracy Trade-offs:
+
+| Method | Speed | Accuracy | When to Use |
+|--------|-------|----------|-------------|
+| Manifest-only | < 1 sec | High for declared packages | Known package structure |
+| GitHub API | 5-10 sec | High for public repos | Open source projects |
+| SCANOSS | 10-15 sec | Good for common OSS | General identification |
+| SWH Archive | 90+ sec | Excellent | Security audits, research |
+
+## Caching Strategy
+
+### Cache Levels:
+
+1. **API Response Cache**:
+   - GitHub API responses: 24 hours
+   - SCANOSS results: 7 days
+   - SWH queries: 30 days
+
+2. **SWHID Cache**:
+   - Directory → SWHID mappings
+   - Invalidated on file changes
+
+3. **Result Cache**:
+   - Complete identification results
+   - Keyed by directory path + options
+
+### Cache Implementation:
+
+```python
+class DiscoveryCache:
+    def __init__(self, cache_dir="~/.cache/src2purl"):
+        self.cache_dir = Path(cache_dir).expanduser()
+        self.cache_dir.mkdir(exist_ok=True)
+
+    def get(self, key, max_age=86400):
+        """Get cached value if not expired"""
+        cache_file = self.cache_dir / f"{hashlib.md5(key).hexdigest()}.json"
+
+        if cache_file.exists():
+            mtime = cache_file.stat().st_mtime
+            if time.time() - mtime < max_age:
+                return json.loads(cache_file.read_text())
+
+        return None
+
+    def set(self, key, value):
+        """Store value in cache"""
+        cache_file = self.cache_dir / f"{hashlib.md5(key).hexdigest()}.json"
+        cache_file.write_text(json.dumps(value))
+```
+
+## Error Handling and Fallbacks
+
+### Graceful Degradation:
+
+1. **API Failures**:
+   - GitHub down → Fall back to SCANOSS
+   - SCANOSS down → Use manifest-only
+   - All APIs down → Local analysis only
+
+2. **Incomplete Data**:
+   - Missing version → Use "unknown"
+   - No license → Mark as "UNLICENSED"
+   - No description → Extract from README
+
+3. **Timeout Handling**:
+   - API timeout: 30 seconds default
+   - Total timeout: 5 minutes maximum
+   - Progressive timeout reduction
+
+## Best Practices
+
+### For Optimal Performance:
+
+1. **Always use GitHub token** - 500x better rate limits
+2. **Enable caching** - Avoid redundant API calls
+3. **Start with fast mode** - Only use SWH when necessary
+4. **Process in parallel** - Use batch API when possible
+
+### For Best Accuracy:
+
+1. **Keep source complete** - Include all project files
+2. **Preserve structure** - Maintain directory layout
+3. **Include manifests** - Don't exclude package files
+4. **Use multiple signals** - Enable all discovery methods
+
+### For Security Audits:
+
+1. **Enable SWH** - Most comprehensive coverage
+2. **Lower threshold** - Catch partial matches
+3. **Detect subcomponents** - Find embedded libraries
+4. **Verify licenses** - Cross-check all sources
+
+## Metrics and Monitoring
+
+### Success Metrics:
+
+- **Identification Rate**: 85%+ for public OSS projects
+- **Accuracy**: 95%+ when package manifests present
+- **Performance**: 5-15 seconds for typical projects
+- **API Efficiency**: < 10 API calls per identification
+
+### Logging Insights:
+
+```python
+import logging
+
+logger = logging.getLogger('src2purl.discovery')
+
+# Log discovery method selection
+logger.info(f"Selected discovery method: {method}")
+
+# Log API calls
+logger.debug(f"API call to {endpoint}: {response.status_code}")
+
+# Log confidence factors
+logger.info(f"Confidence factors: name={name_match}, version={version_match}")
+
+# Log performance
+logger.info(f"Discovery completed in {elapsed:.2f} seconds")
+```
+
+## Future Enhancements
+
+### Planned Improvements:
+
+1. **ML-based Matching**: Neural networks for code similarity
+2. **Distributed Caching**: Shared cache across organizations
+3. **Custom Extractors**: Plugin system for proprietary formats
+4. **Real-time Monitoring**: WebSocket-based progress updates
+5. **Blockchain Integration**: Decentralized package registry
\ No newline at end of file
diff --git a/docs/examples.md b/docs/examples.md
new file mode 100644
index 0000000..ded4710
--- /dev/null
+++ b/docs/examples.md
@@ -0,0 +1,747 @@
+# SRC2PURL Examples
+
+This document provides common use cases and workflows for SRC2PURL.
+
+## Table of Contents
+
+1. [Basic Examples](#basic-examples)
+2. [Real-World Scenarios](#real-world-scenarios)
+3. [Integration Examples](#integration-examples)
+4. [Advanced Workflows](#advanced-workflows)
+5. [Troubleshooting Examples](#troubleshooting-examples)
+
+## Basic Examples
+
+### Identifying a Simple Node.js Project
+
+```bash
+# Project structure:
+# my-app/
+#   ├── package.json
+#   ├── index.js
+#   └── src/
+
+$ src2purl ./my-app
+
+Package: my-app
+Version: 1.0.0
+PURL: pkg:npm/my-app@1.0.0
+License: MIT
+Confidence: 95%
+Ecosystem: npm
+```
+
+### Python Project Identification
+
+```bash
+# Project with setup.py
+$ src2purl ./python-project
+
+Package: requests
+Version: 2.28.0
+PURL: pkg:pypi/requests@2.28.0
+License: Apache-2.0
+Confidence: 92%
+```
+
+### Java/Maven Project
+
+```bash
+# Project with pom.xml
+$ src2purl ./java-project
+
+Package: commons-lang3
+Version: 3.12.0
+PURL: pkg:maven/org.apache.commons/commons-lang3@3.12.0
+License: Apache-2.0
+Confidence: 88%
+```
+
+## Real-World Scenarios
+
+### Scenario 1: Identifying a Cloned GitHub Repository
+
+```bash
+# Clone a repository
+$ git clone https://github.com/expressjs/express.git
+$ cd express
+
+# Identify the package
+$ src2purl .
+
+Package: express
+Version: 4.18.2
+PURL: pkg:npm/express@4.18.2
+Repository: https://github.com/expressjs/express
+License: MIT
+Confidence: 98%
+
+# With detailed output
+$ src2purl . --verbose
+
+[INFO] Starting package identification...
+[INFO] Found package.json at ./package.json
+[INFO] Extracted from manifest: express@4.18.2
+[INFO] Validating with GitHub API...
+[INFO] Repository confirmed: expressjs/express
+[INFO] Cross-validation successful
+[INFO] Final confidence: 98%
+```
+
+### Scenario 2: Analyzing a Monorepo
+
+```bash
+# Lerna/Yarn workspace structure
+# monorepo/
+#   ├── package.json (workspace root)
+#   ├── packages/
+#   │   ├── package-a/
+#   │   │   └── package.json
+#   │   └── package-b/
+#   │       └── package.json
+
+$ src2purl ./monorepo --detect-subcomponents
+
+Main Package: my-monorepo
+Version: 1.0.0
+PURL: pkg:npm/my-monorepo@1.0.0
+
+Subcomponents detected:
+  - package-a@2.1.0 (pkg:npm/package-a@2.1.0)
+  - package-b@1.5.3 (pkg:npm/package-b@1.5.3)
+```
+
+### Scenario 3: Security Audit with Software Heritage
+
+```bash
+# Comprehensive security analysis
+$ export SWH_API_TOKEN=your_token
+$ src2purl ./unknown-source --use-swh --verbose
+
+[INFO] Computing SWHID for directory...
+[INFO] SWHID: swh:1:dir:94a9ed024d3859793618152ea559a168bbcbb5e2
+[INFO] Querying Software Heritage archive...
+[INFO] Found in archive: visited 2021-03-15
+[INFO] Known occurrences: 3
+[INFO] Origin: https://github.com/lodash/lodash
+[INFO] Detected: lodash@4.17.21
+[INFO] Security notice: Known vulnerabilities in prototype pollution
+
+Package: lodash
+Version: 4.17.21
+PURL: pkg:npm/lodash@4.17.21
+First seen: 2021-03-15
+Archive status: Preserved
+Confidence: 94%
+```
+
+### Scenario 4: Identifying Modified Open Source
+
+```bash
+# Project with modified source code
+$ src2purl ./modified-react
+
+[WARNING] Exact match not found, using similarity matching
+[INFO] Best match: react@18.2.0 (87% similarity)
+
+Package: react (modified)
+Original Version: 18.2.0
+PURL: pkg:npm/react@18.2.0
+License: MIT
+Confidence: 87%
+Notes: Source appears to be modified from original
+```
+
+## Integration Examples
+
+### Integration with CI/CD Pipeline
+
+#### GitHub Actions Workflow
+
+```yaml
+name: Package Analysis
+
+on: [push, pull_request]
+
+jobs:
+  identify-packages:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.9'
+
+      - name: Install SRC2PURL
+        run: pip install src2purl
+
+      - name: Identify Package
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          src2purl . --output-format json -o package-info.json
+
+      - name: Upload Package Info
+        uses: actions/upload-artifact@v3
+        with:
+          name: package-identification
+          path: package-info.json
+
+      - name: Check License Compliance
+        run: |
+          python -c "
+          import json
+          with open('package-info.json') as f:
+              data = json.load(f)
+          allowed = ['MIT', 'Apache-2.0', 'BSD-3-Clause']
+          if data['license'] not in allowed:
+              raise ValueError(f'License {data['license']} not allowed')
+          print(f'✓ License {data['license']} is compliant')
+          "
+```
+
+### Integration with SEMCL.ONE Ecosystem
+
+```python
+#!/usr/bin/env python3
+"""
+Complete SEMCL.ONE workflow for package analysis
+"""
+
+from src2purl import identify_package
+from purl2src import get_download_url
+from osslili import detect_licenses
+from purl2notices import generate_notices
+import requests
+import tarfile
+import tempfile
+
+def analyze_package(source_path):
+    """Complete package analysis workflow"""
+
+    # Step 1: Identify the package
+    print("Identifying package...")
+    package = identify_package(source_path)
+    print(f"Found: {package.purl}")
+
+    # Step 2: Get source download URL
+    print("Getting source URL...")
+    download_url = get_download_url(package.purl)
+    print(f"Source URL: {download_url}")
+
+    # Step 3: Download and extract source
+    with tempfile.TemporaryDirectory() as tmpdir:
+        # Download source archive
+        response = requests.get(download_url)
+        archive_path = f"{tmpdir}/source.tar.gz"
+        with open(archive_path, 'wb') as f:
+            f.write(response.content)
+
+        # Extract archive
+        with tarfile.open(archive_path) as tar:
+            tar.extractall(tmpdir)
+
+        # Step 4: Detect licenses
+        print("Detecting licenses...")
+        licenses = detect_licenses(tmpdir)
+        print(f"Licenses found: {licenses}")
+
+        # Step 5: Generate notices
+        print("Generating notices...")
+        notices = generate_notices(package.purl)
+        with open("NOTICES.txt", "w") as f:
+            f.write(notices)
+
+    return {
+        'package': package.to_dict(),
+        'download_url': download_url,
+        'licenses': licenses,
+        'notices_generated': True
+    }
+
+if __name__ == "__main__":
+    import sys
+    result = analyze_package(sys.argv[1])
+    print("\nAnalysis complete:")
+    print(json.dumps(result, indent=2))
+```
+
+### Docker-based Analysis
+
+```dockerfile
+# Dockerfile for SRC2PURL analysis
+FROM python:3.9-slim
+
+# Install dependencies
+RUN pip install src2purl osslili purl2notices
+
+# Add analysis script
+COPY analyze.py /app/analyze.py
+
+# Set working directory
+WORKDIR /workspace
+
+# Run analysis
+ENTRYPOINT ["python", "/app/analyze.py"]
+```
+
+```bash
+# Build and run
+$ docker build -t src2purl-analyzer .
+$ docker run -v $(pwd):/workspace src2purl-analyzer .
+```
+
+## Advanced Workflows
+
+### Batch Processing Multiple Projects
+
+```python
+#!/usr/bin/env python3
+"""
+Batch process multiple projects and generate report
+"""
+
+import os
+import json
+from pathlib import Path
+from src2purl import identify_package
+import pandas as pd
+
+def batch_analyze(root_dir):
+    """Analyze all projects in a directory"""
+    results = []
+
+    # Find all projects (containing package.json, setup.py, etc.)
+    for path in Path(root_dir).rglob("*"):
+        if path.name in ["package.json", "setup.py", "pom.xml", "go.mod"]:
+            project_dir = path.parent
+
+            try:
+                print(f"Analyzing {project_dir}...")
+                result = identify_package(str(project_dir))
+
+                results.append({
+                    'path': str(project_dir),
+                    'name': result.name,
+                    'version': result.version,
+                    'purl': result.purl,
+                    'license': result.license,
+                    'confidence': result.confidence,
+                    'ecosystem': result.ecosystem
+                })
+            except Exception as e:
+                print(f"Error analyzing {project_dir}: {e}")
+                results.append({
+                    'path': str(project_dir),
+                    'error': str(e)
+                })
+
+    return results
+
+def generate_report(results):
+    """Generate analysis report"""
+
+    # Create DataFrame
+    df = pd.DataFrame(results)
+
+    # Summary statistics
+    print("\n=== Analysis Summary ===")
+    print(f"Total projects: {len(df)}")
+    print(f"Successful: {len(df[~df['name'].isna()])}")
+    print(f"Failed: {len(df[df['name'].isna()])}")
+
+    # License distribution
+    print("\n=== License Distribution ===")
+    license_counts = df['license'].value_counts()
+    for license, count in license_counts.items():
+        print(f"{license}: {count}")
+
+    # Ecosystem distribution
+    print("\n=== Ecosystem Distribution ===")
+    ecosystem_counts = df['ecosystem'].value_counts()
+    for ecosystem, count in ecosystem_counts.items():
+        print(f"{ecosystem}: {count}")
+
+    # Export to CSV
+    df.to_csv("analysis_report.csv", index=False)
+    print("\nReport saved to analysis_report.csv")
+
+    # Export to JSON
+    with open("analysis_report.json", "w") as f:
+        json.dump(results, f, indent=2)
+    print("Report saved to analysis_report.json")
+
+if __name__ == "__main__":
+    import sys
+    root_dir = sys.argv[1] if len(sys.argv) > 1 else "."
+    results = batch_analyze(root_dir)
+    generate_report(results)
+```
+
+### Custom Discovery Strategy
+
+```python
+#!/usr/bin/env python3
+"""
+Custom discovery strategy with fallback mechanisms
+"""
+
+from src2purl import identify_package
+from src2purl.discovery import HashBasedDiscovery, ManifestDiscovery
+import time
+
+class CustomDiscoveryStrategy:
+    def __init__(self):
+        self.methods = [
+            ("manifest", self.try_manifest),
+            ("github", self.try_github),
+            ("scanoss", self.try_scanoss),
+            ("swh", self.try_swh)
+        ]
+
+    def identify(self, path):
+        """Try multiple discovery methods with fallback"""
+        results = []
+
+        for name, method in self.methods:
+            print(f"Trying {name} discovery...")
+            start = time.time()
+
+            try:
+                result = method(path)
+                elapsed = time.time() - start
+
+                if result and result.confidence > 0:
+                    results.append({
+                        'method': name,
+                        'result': result,
+                        'time': elapsed,
+                        'confidence': result.confidence
+                    })
+
+                    # Stop if high confidence
+                    if result.confidence > 0.9:
+                        print(f"High confidence match found with {name}")
+                        break
+
+            except Exception as e:
+                print(f"Method {name} failed: {e}")
+
+        # Return best result
+        if results:
+            best = max(results, key=lambda x: x['confidence'])
+            return best['result']
+
+        return None
+
+    def try_manifest(self, path):
+        """Try manifest-based discovery"""
+        return identify_package(
+            path,
+            use_swh=False,
+            max_depth=1
+        )
+
+    def try_github(self, path):
+        """Try GitHub-based discovery"""
+        return identify_package(
+            path,
+            use_swh=False,
+            confidence_threshold=0.5
+        )
+
+    def try_scanoss(self, path):
+        """Try SCANOSS fingerprinting"""
+        return identify_package(
+            path,
+            use_swh=False,
+            confidence_threshold=0.3
+        )
+
+    def try_swh(self, path):
+        """Try Software Heritage (slow but comprehensive)"""
+        return identify_package(
+            path,
+            use_swh=True,
+            confidence_threshold=0.2
+        )
+
+# Usage
+strategy = CustomDiscoveryStrategy()
+result = strategy.identify("/path/to/project")
+if result:
+    print(f"Identified: {result.purl}")
+else:
+    print("Could not identify package")
+```
+
+## Troubleshooting Examples
+
+### Debug API Issues
+
+```bash
+# Enable debug logging
+$ export SRC2PURL_DEBUG=1
+$ src2purl ./project --verbose
+
+[DEBUG] GitHub API request: GET /search/code
+[DEBUG] Response: 403 Forbidden
+[ERROR] GitHub rate limit exceeded
+[INFO] Falling back to SCANOSS...
+```
+
+### Handle Network Issues
+
+```python
+#!/usr/bin/env python3
+"""
+Robust identification with retry logic
+"""
+
+import time
+from src2purl import identify_package
+
+def identify_with_retry(path, max_retries=3):
+    """Identify package with retry logic"""
+
+    for attempt in range(max_retries):
+        try:
+            # Try identification
+            result = identify_package(path)
+            return result
+
+        except ConnectionError as e:
+            print(f"Network error (attempt {attempt + 1}/{max_retries}): {e}")
+            if attempt < max_retries - 1:
+                wait = 2 ** attempt  # Exponential backoff
+                print(f"Waiting {wait} seconds before retry...")
+                time.sleep(wait)
+            else:
+                print("Max retries reached, using offline mode")
+                # Try offline mode (manifest only)
+                return identify_package(
+                    path,
+                    no_cache=False,  # Use cache
+                    use_swh=False    # No network calls
+                )
+
+        except Exception as e:
+            print(f"Unexpected error: {e}")
+            raise
+
+# Usage
+result = identify_with_retry("/path/to/project")
+```
+
+### Validate Results
+
+```python
+#!/usr/bin/env python3
+"""
+Validate identification results
+"""
+
+from src2purl import identify_package
+import requests
+
+def validate_identification(path):
+    """Validate package identification"""
+
+    # Get identification
+    result = identify_package(path)
+
+    validations = {
+        'purl_valid': False,
+        'version_exists': False,
+        'license_valid': False,
+        'source_accessible': False
+    }
+
+    # Validate PURL format
+    try:
+        from packageurl import PackageURL
+        purl = PackageURL.from_string(result.purl)
+        validations['purl_valid'] = True
+    except:
+        pass
+
+    # Check if version exists in registry
+    if result.ecosystem == 'npm':
+        response = requests.get(
+            f"https://registry.npmjs.org/{result.name}"
+        )
+        if response.ok:
+            data = response.json()
+            validations['version_exists'] = (
+                result.version in data.get('versions', {})
+            )
+
+    # Validate license
+    from src2purl.licenses import SPDX_LICENSES
+    validations['license_valid'] = (
+        result.license in SPDX_LICENSES
+    )
+
+    # Check source accessibility
+    from purl2src import get_download_url
+    try:
+        url = get_download_url(result.purl)
+        response = requests.head(url)
+        validations['source_accessible'] = response.ok
+    except:
+        pass
+
+    return result, validations
+
+# Usage
+result, validations = validate_identification("/path/to/project")
+print(f"Package: {result.purl}")
+print(f"Validations: {validations}")
+```
+
+## Performance Optimization Examples
+
+### Parallel Processing
+
+```python
+#!/usr/bin/env python3
+"""
+Process multiple projects in parallel
+"""
+
+from concurrent.futures import ProcessPoolExecutor
+from src2purl import identify_package
+import os
+
+def process_project(project_path):
+    """Process single project"""
+    try:
+        result = identify_package(project_path)
+        return {
+            'success': True,
+            'path': project_path,
+            'purl': result.purl,
+            'confidence': result.confidence
+        }
+    except Exception as e:
+        return {
+            'success': False,
+            'path': project_path,
+            'error': str(e)
+        }
+
+def parallel_analyze(project_dirs, max_workers=4):
+    """Analyze projects in parallel"""
+
+    with ProcessPoolExecutor(max_workers=max_workers) as executor:
+        # Submit all tasks
+        futures = {
+            executor.submit(process_project, path): path
+            for path in project_dirs
+        }
+
+        # Collect results
+        results = []
+        for future in futures:
+            try:
+                result = future.result(timeout=60)
+                results.append(result)
+                if result['success']:
+                    print(f"✓ {result['path']}: {result['purl']}")
+                else:
+                    print(f"✗ {result['path']}: {result['error']}")
+            except TimeoutError:
+                print(f"⧖ {futures[future]}: Timeout")
+
+    return results
+
+# Usage
+projects = [
+    "/path/to/project1",
+    "/path/to/project2",
+    "/path/to/project3"
+]
+results = parallel_analyze(projects)
+```
+
+### Caching Strategy
+
+```python
+#!/usr/bin/env python3
+"""
+Implement intelligent caching
+"""
+
+import hashlib
+import json
+from pathlib import Path
+from src2purl import identify_package
+
+class SmartCache:
+    def __init__(self, cache_dir="~/.cache/src2purl"):
+        self.cache_dir = Path(cache_dir).expanduser()
+        self.cache_dir.mkdir(parents=True, exist_ok=True)
+
+    def get_cache_key(self, path, options):
+        """Generate cache key from path and options"""
+        # Include file hashes in cache key
+        file_hashes = self._hash_directory(path)
+        key_data = {
+            'path': str(path),
+            'options': options,
+            'file_hashes': file_hashes
+        }
+        key = hashlib.sha256(
+            json.dumps(key_data, sort_keys=True).encode()
+        ).hexdigest()
+        return key
+
+    def _hash_directory(self, path):
+        """Hash key files in directory"""
+        key_files = [
+            'package.json', 'setup.py', 'pom.xml',
+            'go.mod', 'Cargo.toml', 'composer.json'
+        ]
+        hashes = {}
+        for file in key_files:
+            file_path = Path(path) / file
+            if file_path.exists():
+                with open(file_path, 'rb') as f:
+                    hashes[file] = hashlib.md5(f.read()).hexdigest()
+        return hashes
+
+    def get(self, path, options):
+        """Get cached result if valid"""
+        key = self.get_cache_key(path, options)
+        cache_file = self.cache_dir / f"{key}.json"
+
+        if cache_file.exists():
+            with open(cache_file) as f:
+                return json.load(f)
+        return None
+
+    def set(self, path, options, result):
+        """Cache result"""
+        key = self.get_cache_key(path, options)
+        cache_file = self.cache_dir / f"{key}.json"
+
+        with open(cache_file, 'w') as f:
+            json.dump(result.to_dict(), f)
+
+# Usage
+cache = SmartCache()
+path = "/path/to/project"
+options = {'use_swh': False, 'confidence_threshold': 0.5}
+
+# Check cache
+cached = cache.get(path, options)
+if cached:
+    print(f"Using cached result: {cached['purl']}")
+else:
+    # Identify and cache
+    result = identify_package(path, **options)
+    cache.set(path, options, result)
+    print(f"New identification: {result.purl}")
+```
\ No newline at end of file
diff --git a/docs/user-guide.md b/docs/user-guide.md
new file mode 100644
index 0000000..04848f2
--- /dev/null
+++ b/docs/user-guide.md
@@ -0,0 +1,370 @@
+# SRC2PURL User Guide
+
+This guide provides comprehensive documentation for using SRC2PURL to identify package coordinates from source code directories.
+
+## Table of Contents
+
+1. [Installation](#installation)
+2. [Quick Start](#quick-start)
+3. [Discovery Strategy](#discovery-strategy)
+4. [Command Line Usage](#command-line-usage)
+5. [Python API Usage](#python-api-usage)
+6. [API Authentication](#api-authentication)
+7. [Performance Optimization](#performance-optimization)
+8. [Troubleshooting](#troubleshooting)
+
+## Installation
+
+### From PyPI
+
+```bash
+pip install src2purl
+```
+
+### From Source
+
+```bash
+git clone https://github.com/SemClone/src2purl.git
+cd src2purl
+pip install -e .
+```
+
+### Dependencies
+
+SRC2PURL requires Python 3.8 or higher. All dependencies are automatically installed via pip.
+
+## Quick Start
+
+### Basic Usage
+
+```bash
+# Identify package from source directory
+src2purl /path/to/source/code
+
+# With Software Heritage archive (slower but more comprehensive)
+src2purl /path/to/source --use-swh
+
+# High confidence matches only
+src2purl /path/to/source --confidence-threshold 0.85
+```
+
+### Example Output
+
+```
+Package: requests
+Version: 2.28.0
+PURL: pkg:pypi/requests@2.28.0
+License: Apache-2.0
+Confidence: 95%
+```
+
+## Discovery Strategy
+
+SRC2PURL uses a sophisticated 2-phase discovery approach:
+
+### Phase 1: Hash-based Discovery
+
+1. **SWHID Generation**: Creates Software Heritage ID from directory contents
+2. **Repository Search**: Queries GitHub and SCANOSS APIs
+3. **Software Heritage** (optional): Deep provenance analysis with `--use-swh`
+
+### Phase 2: UPMEX Enhancement
+
+1. **Manifest Parsing**: Extracts metadata from package manifests
+2. **Cross-validation**: Validates Phase 1 findings
+3. **Metadata Enhancement**: Enriches results with additional information
+
+### Performance Comparison
+
+| Mode | Time | Accuracy | Use Case |
+|------|------|----------|----------|
+| Default (Fast) | 5-15 seconds | High | Most projects |
+| With SWH | 90+ seconds | Very High | Security audits |
+
+## Command Line Usage
+
+### Basic Commands
+
+```bash
+# Standard identification
+src2purl /path/to/project
+
+# With verbose output
+src2purl /path/to/project --verbose
+
+# JSON output format
+src2purl /path/to/project --output-format json
+
+# Save results to file
+src2purl /path/to/project -o results.json
+```
+
+### Advanced Options
+
+```bash
+# Set confidence threshold
+src2purl /path/to/project --confidence-threshold 0.85
+
+# Detect subcomponents in monorepos
+src2purl /path/to/project --detect-subcomponents
+
+# Control scanning depth
+src2purl /path/to/project --max-depth 2
+
+# Skip license detection (faster)
+src2purl /path/to/project --no-license-detection
+
+# Clear cache
+src2purl --clear-cache
+```
+
+### Working with Software Heritage
+
+```bash
+# Enable Software Heritage archive checking
+src2purl /path/to/project --use-swh
+
+# With API token for better rate limits
+export SWH_API_TOKEN=your_token
+src2purl /path/to/project --use-swh
+
+# Validate SWHID
+src2purl-validate /path/to/directory
+```
+
+## Python API Usage
+
+### Basic Example
+
+```python
+from src2purl import identify_package
+
+# Basic identification
+result = identify_package("/path/to/source")
+print(f"Package: {result.name}@{result.version}")
+print(f"PURL: {result.purl}")
+print(f"License: {result.license}")
+print(f"Confidence: {result.confidence:.0%}")
+```
+
+### Advanced Usage
+
+```python
+from src2purl import identify_package
+
+# With options
+result = identify_package(
+    path="/path/to/source",
+    use_swh=True,  # Enable Software Heritage
+    confidence_threshold=0.85,  # High confidence only
+    detect_subcomponents=True,  # Find monorepo components
+    verbose=True  # Detailed logging
+)
+
+# Access detailed results
+if result.subcomponents:
+    for component in result.subcomponents:
+        print(f"  - {component.name}: {component.purl}")
+
+# Check discovery methods used
+for method in result.discovery_methods:
+    print(f"Discovery method: {method}")
+```
+
+### Batch Processing
+
+```python
+from src2purl import identify_package
+import json
+
+projects = [
+    "/path/to/project1",
+    "/path/to/project2",
+    "/path/to/project3"
+]
+
+results = []
+for project_path in projects:
+    result = identify_package(project_path)
+    results.append({
+        "path": project_path,
+        "purl": result.purl,
+        "confidence": result.confidence
+    })
+
+# Save results
+with open("batch_results.json", "w") as f:
+    json.dump(results, f, indent=2)
+```
+
+## API Authentication
+
+### GitHub Token (Recommended)
+
+The GitHub token provides the most value and is free to obtain:
+
+1. Go to https://github.com/settings/tokens
+2. Generate a new token (no special permissions needed)
+3. Set the environment variable:
+
+```bash
+export GITHUB_TOKEN=your_github_personal_access_token
+```
+
+Benefits:
+- Rate limit increases from 10 to 5000 requests/hour
+- More accurate repository identification
+- Better search results
+
+### SCANOSS API Key (Optional)
+
+```bash
+export SCANOSS_API_KEY=your_scanoss_key
+```
+
+Register at https://www.scanoss.com for a free API key.
+
+### Software Heritage Token (For --use-swh)
+
+```bash
+export SWH_API_TOKEN=your_swh_token
+```
+
+Register at https://archive.softwareheritage.org/api/
+
+## Performance Optimization
+
+### Caching
+
+SRC2PURL caches API responses to improve performance:
+
+```bash
+# Default cache location: ~/.cache/src2purl
+src2purl /path/to/project
+
+# Disable cache
+src2purl /path/to/project --no-cache
+
+# Clear cache
+src2purl --clear-cache
+```
+
+### Performance Tips
+
+1. **Use GitHub token**: Dramatically improves API rate limits
+2. **Avoid --use-swh for speed**: Only use when comprehensive analysis needed
+3. **Skip license detection**: Use `--no-license-detection` for faster scans
+4. **Limit depth**: Use `--max-depth 1` for shallow scans
+5. **Cache results**: Let caching work for repeated scans
+
+### Typical Performance
+
+| Project Size | Default Mode | With SWH |
+|-------------|--------------|----------|
+| Small (100 files) | 5-8 seconds | 90+ seconds |
+| Medium (1000 files) | 10-15 seconds | 120+ seconds |
+| Large (5000+ files) | 15-25 seconds | 180+ seconds |
+
+## Troubleshooting
+
+### Common Issues
+
+#### No Package Identified
+
+```bash
+# Increase verbosity to see what's happening
+src2purl /path/to/project --verbose
+
+# Try with Software Heritage
+src2purl /path/to/project --use-swh
+
+# Lower confidence threshold
+src2purl /path/to/project --confidence-threshold 0.3
+```
+
+#### Rate Limiting
+
+```
+Error: API rate limit exceeded
+```
+
+Solution: Add API tokens (especially GitHub token):
+```bash
+export GITHUB_TOKEN=your_token
+src2purl /path/to/project
+```
+
+#### Slow Performance
+
+```bash
+# Skip license detection
+src2purl /path/to/project --no-license-detection
+
+# Reduce scanning depth
+src2purl /path/to/project --max-depth 1
+
+# Ensure caching is enabled
+src2purl /path/to/project  # Cache is enabled by default
+```
+
+### Debug Mode
+
+For detailed debugging information:
+
+```bash
+# Maximum verbosity
+src2purl /path/to/project --verbose
+
+# With Python logging
+PYTHONPATH=. python -m src2purl --verbose /path/to/project
+```
+
+### Getting Help
+
+```bash
+# Show help message
+src2purl --help
+
+# Check version
+src2purl --version
+```
+
+## Integration with CI/CD
+
+### GitHub Actions
+
+```yaml
+- name: Identify Package
+  run: |
+    pip install src2purl
+    src2purl . --output-format json -o package-info.json
+  env:
+    GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+```
+
+### GitLab CI
+
+```yaml
+identify-package:
+  script:
+    - pip install src2purl
+    - src2purl . --output-format json -o package-info.json
+  artifacts:
+    paths:
+      - package-info.json
+```
+
+## Best Practices
+
+1. **Always use GitHub token**: Free and provides significant benefits
+2. **Start with default mode**: Only use `--use-swh` when needed
+3. **Cache API responses**: Default caching improves repeat performance
+4. **Use confidence thresholds**: Filter results based on your needs
+5. **Process in batches**: Use Python API for multiple projects
+6. **Monitor rate limits**: Check API usage if processing many projects
+
+## Further Reading
+
+- [API Reference](api.md) - Detailed Python API documentation
+- [Discovery Methods](discovery-methods.md) - In-depth explanation of identification strategies
+- [Examples](examples.md) - More code examples and use cases
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