refactor(examples): code analysis engine

changes:
  - file: advanced_usage_examples.py
    area: core
    added: [example_4_batch_processing, example_5_custom_metrics, example_2_focus_area_strategies, example_1_custom_file_patterns, example_6_workflow_automation, main, +1 more]
  - file: cli_command_examples.py
    area: cli
    added: [run_command, main]
  - file: external_tools_examples.py
    area: util
    added: [example_2_run_individual_tools, example_5_custom_analysis, example_1_check_external_tools, example_3_run_all_tools, example_4_generate_strategy_with_tools, main]
  - file: integrated_functionality_examples.py
    area: core
    added: [example_2_template_generation, example_7_external_tools, example_3_strategy_comparison, example_5_strategy_stats, main, example_4_export_formats, +2 more]
  - file: quick_start_examples.py
    area: core
    added: [quick_start_4, quick_start_1, quick_start_2, quick_start_5, quick_start_3, main]
  - file: file_analyzer.py
    area: analyzer
    modified: [_extract_from_json_structure, _analyze_toon, _analyze_text, _analyze_json, _extract_from_yaml_structure, FileAnalyzer, +3 more]
  - file: generator.py
    area: analyzer
    modified: [_generate_goal, _generate_tasks, _make_serializable, PlanfileGenerator, _generate_target_metrics, _generate_quality_gates, +9 more]
  - file: metrics_extractor.py
    area: analyzer
    added: [_extract_critical_metrics, _extract_cc_metrics, _extract_duplication_metrics, extract_key_metrics, _extract_coverage_metrics, _extract_validation_metrics]
  - file: strategy_builder.py
    area: analyzer
    added: [generate_tasks, parse_effort, generate_quality_gates, generate_risks, generate_success_criteria, generate_target_metrics, +2 more]
  - file: json_parser.py
    area: analyzer
    added: [analyze_json]
  - file: text_parser.py
    area: analyzer
    added: [analyze_text]
  - file: toon_parser.py
    area: analyzer
    added: [_parse_toon_header, _parse_toon_sections, analyze_toon]
  - file: yaml_parser.py
    area: analyzer
    added: [extract_from_yaml_structure, analyze_yaml]
  - file: cmd_apply.py
    area: cli
    added: [_execute_apply_strategy, apply_strategy_cli, _display_apply_results, _save_results]
  - file: cmd_generate.py
    area: cli
    added: [generate_strategy_cli, generate_from_files_cmd]
  - file: cmd_review.py
    area: cli
    added: [review_strategy_cli]
  - file: cmd_utils.py
    area: cli
    added: [_select_backend, _load_backend_config, _load_and_validate_strategy, _parse_sprint_filter, get_backend]
  - file: cmd_validate.py
    area: cli
    added: [validate_strategy_cli]
  - file: commands.py
    area: cli
    removed: [validate_strategy_cli, _load_backend_config, _load_and_validate_strategy, _display_apply_results, _execute_apply_strategy, review_strategy_cli, +7 more]

dependencies:
  flow: "external_tools_examples→generator→file_analyzer, advanced_usage_examples→generator→file_analyzer, toon_parser→text_parser, integrated_functionality_examples→generator→file_analyzer, json_parser→yaml_parser→text_parser, quick_start_examples→generator→file_analyzer"
  - advanced_usage_examples.py -> generator.py
  - external_tools_examples.py -> generator.py
  - integrated_functionality_examples.py -> generator.py
  - quick_start_examples.py -> generator.py
  - generator.py -> file_analyzer.py
  - json_parser.py -> yaml_parser.py
  - toon_parser.py -> text_parser.py
  - yaml_parser.py -> text_parser.py

stats:
  lines: "+5027/-1184 (net +3843)"
  files: 27
  complexity: "+127% complexity (monitor)"

Author: tom-sapletta-com

CHANGELOG.md

@@ -7,6 +7,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.1.26] - 2026-03-26
+
+### Docs
+- Update TODO.md
+- Update examples/EXAMPLES_REORGANIZATION.md
+- Update examples/README.md
+- Update examples/advanced-usage/README.md
+- Update examples/cli-commands/README.md
+- Update examples/external-tools/README.md
+- Update examples/integrated-functionality/README.md
+- Update examples/quick-start/README.md
+
+### Other
+- Update examples/advanced-usage/advanced_usage_examples.py
+- Update examples/advanced-usage/run.sh
+- Update examples/cli-commands/cli_command_examples.py
+- Update examples/cli-commands/run.sh
+- Update examples/external-tools/external_tools_examples.py
+- Update examples/external-tools/run.sh
+- Update examples/integrated-functionality/integrated_functionality_examples.py
+- Update examples/integrated-functionality/run.sh
+- Update examples/quick-start.yaml
+- Update examples/quick-start/quick_start_examples.py
+- ... and 20 more files
+
 ## [0.1.25] - 2026-03-26
 
 ### Docs

TODO.md

@@ -0,0 +1,15 @@
+# Planfile TODO List
+
+## Completed Tasks
+- [x] Identify and remove unnecessary and generated files (`htmlcov/`, `.coverage`, etc.)
+- [x] Organize generated markdown summaries into `docs/summaries/` directory
+- [x] Run projects in `examples/*` to ensure base correctness
+- [x] Refactor `planfile/analysis/file_analyzer.py` (God module)
+- [x] Refactor `planfile/analysis/generator.py` (God module)
+- [x] Refactor `planfile/cli/commands.py` (God module)
+- [x] Split highest-CC functions (e.g., `_analyze_toon`, `_extract_key_metrics`)
+- [x] Preserve module boundaries and update imports/exports as per `map.toon.yaml`
+
+## Pending Improvements
+- [ ] Implement `--version` flag for the CLI to display the current version.
+- [ ] Add an extensible Backend Registry to remove complex `if/elif` statements when creating integrations.

VERSION

@@ -1 +1 @@
-0.1.25
+0.1.26

examples/EXAMPLES_REORGANIZATION.md

@@ -0,0 +1,91 @@
+# Examples Reorganization Summary
+
+## What Was Done
+
+Reorganized all new examples into separate folders with consistent structure:
+
+```
+examples/
+├── quick-start/               # Beginner friendly examples
+│   ├── README.md
+│   ├── run.sh
+│   └── quick_start_examples.py
+├── integrated-functionality/  # Complete feature demo
+│   ├── README.md
+│   ├── run.sh
+│   └── integrated_functionality_examples.py
+├── cli-commands/              # CLI command showcase
+│   ├── README.md
+│   ├── run.sh
+│   └── cli_command_examples.py
+├── external-tools/           # External tools integration
+│   ├── README.md
+│   ├── run.sh
+│   └── external_tools_examples.py
+└── advanced-usage/           # Advanced patterns
+    ├── README.md
+    ├── run.sh
+    └── advanced_usage_examples.py
+```
+
+## Benefits
+
+1. **Better Organization** - Each example type has its own folder
+2. **Consistent Structure** - Every folder has README.md, run.sh, and Python script
+3. **Easy Navigation** - Clear progression from beginner to advanced
+4. **Independent Execution** - Each example can be run independently
+5. **Better Documentation** - Each README is specific to its examples
+
+## How to Use
+
+```bash
+# Quick start for beginners
+cd quick-start && ./run.sh
+
+# Complete functionality overview
+cd integrated-functionality && ./run.sh
+
+# CLI commands demonstration
+cd cli-commands && ./run.sh
+
+# External tools (code2llm, vallm, redup)
+cd external-tools && ./run.sh
+
+# Advanced patterns and workflows
+cd advanced-usage && ./run.sh
+```
+
+## File Changes
+
+### Moved Files
+- `quick_start_examples.py` → `quick-start/`
+- `integrated_functionality_examples.py` → `integrated-functionality/`
+- `cli_command_examples.py` → `cli-commands/`
+- `external_tools_examples.py` → `external-tools/`
+- `advanced_usage_examples.py` → `advanced-usage/`
+
+### Created Files
+- 5 × `README.md` - One for each example folder
+- 5 × `run.sh` - Convenience scripts for each example
+- Updated main `examples/README.md` with new structure
+
+### Updated Files
+- `examples/README.md` - Updated to reflect folder structure
+- Fixed import issue in `file_analyzer.py`
+
+## Testing
+
+All examples have been tested and work correctly:
+- Each `run.sh` script is executable
+- Examples run independently
+- Documentation is clear and accurate
+- Progression from simple to complex is logical
+
+## Next Steps
+
+1. Users can start with `quick-start` for basics
+2. Progress through examples based on needs
+3. Each folder is self-contained
+4. Generated files stay in their respective folders
+
+The examples are now better organized and easier to navigate!

examples/README.md

@@ -27,7 +27,27 @@ examples/
 │   └── simple.yaml
 ├── tasks/                      # Example task patterns
 │   └── common.yaml
-└── run_all_tests.sh           # Master test runner
+├── run_all_tests.sh           # Master test runner
+├── quick-start/               # ⚡ Quick start guide (NEW!)
+│   ├── README.md
+│   ├── run.sh
+│   └── quick_start_examples.py
+├── integrated-functionality/  # 🚀 Integrated features demo
+│   ├── README.md
+│   ├── run.sh
+│   └── integrated_functionality_examples.py
+├── cli-commands/              # 💻 CLI commands showcase
+│   ├── README.md
+│   ├── run.sh
+│   └── cli_command_examples.py
+├── external-tools/           # 🔧 External tools integration
+│   ├── README.md
+│   ├── run.sh
+│   └── external_tools_examples.py
+└── advanced-usage/           # 🎯 Advanced patterns and workflows
+    ├── README.md
+    ├── run.sh
+    └── advanced_usage_examples.py
 ```
 
 ## Quick Start
@@ -48,14 +68,35 @@ pip install litellm llx PyGithub python-gitlab jira
 ### 2. Set Up API Keys
 
 ```bash
+# For OpenAI (if using)
+export OPENAI_API_KEY=sk-...
+
+# For GitHub backend (if using)
+export GITHUB_TOKEN=ghp_...
+
 # For OpenRouter (free LLM validation)
-export OPENROUTER_API_KEY=your_key_here
+export OPENROUTER_API_KEY=sk-or-v1-...
+```
+
+### 3. Run Examples
+
+Each example has its own folder with README and run.sh script:
+
+```bash
+# Quick start (beginners)
+cd quick-start && ./run.sh
+
+# Integrated functionality (complete overview)
+cd integrated-functionality && ./run.sh
+
+# CLI commands (command-line interface)
+cd cli-commands && ./run.sh
+
+# External tools (code2llm, vallm, redup)
+cd external-tools && ./run.sh
 
-# For various backends (optional)
-export GITHUB_TOKEN=your_github_token
-export JIRA_URL=your_jira_url
-export JIRA_EMAIL=your_email
-export JIRA_TOKEN=your_jira_token
+# Advanced usage (power users)
+cd advanced-usage && ./run.sh
 ```
 
 ### 3. Run All Examples with Validation
@@ -117,6 +158,77 @@ Shows metric-driven planning using LLX:
 python ecosystem/04_llx_integration.py
 ```
 
+## New Examples (Integrated Functionality)
+
+### ⚡ Quick Start (quick-start/)
+
+Get started with planfile in minutes! This example shows the basics:
+- Generate strategy from files
+- Create templates
+- Load and analyze strategies
+- Export to different formats
+- Compare strategies
+
+```bash
+cd quick-start && ./run.sh
+```
+
+### 🚀 Integrated Functionality (integrated-functionality/)
+
+Comprehensive demo of all new integrated features:
+- File analysis without external scripts
+- Template generation for different project types
+- Strategy comparison and merging
+- Multiple export formats
+- Statistics and health checking
+
+```bash
+cd integrated-functionality && ./run.sh
+```
+
+### 💻 CLI Commands (cli-commands/)
+
+Shows how to use all new CLI commands:
+- `planfile template` - Generate templates
+- `planfile stats` - View statistics
+- `planfile export` - Export to various formats
+- `planfile compare` - Compare strategies
+- `planfile health` - Check project health
+- `planfile generate-from-files` - Analyze and generate
+
+```bash
+cd cli-commands && ./run.sh
+```
+
+### 🔧 External Tools (external-tools/)
+
+Integration with external analysis tools:
+- code2llm - Code complexity analysis
+- vallm - Validation and linting
+- redup - Code duplication detection
+- Combined analysis with all tools
+
+```bash
+# Install tools first
+pip install code2llm vallm redup
+
+cd external-tools && ./run.sh
+```
+
+### 🎯 Advanced Usage (advanced-usage/)
+
+Advanced patterns and workflows:
+- Custom file patterns
+- Focus-specific strategies
+- Iterative strategy refinement
+- Batch processing multiple directories
+- Custom metrics integration
+- CI/CD workflow automation
+
+```bash
+cd advanced-usage && ./run.sh
+```
+
 ## Validation with LLX
 
 ### Automated Validation
@@ -241,6 +353,94 @@ Each test generates:
 
 ## Example Generated Strategy
 
+## Quick Reference
+
+### New CLI Commands
+```bash
+# Generate template
+planfile template web ecommerce
+
+# Generate from files
+planfile generate-from-files . --focus quality
+
+# View statistics
+planfile stats strategy.yaml
+
+# Export formats
+planfile export strategy.yaml --format html
+planfile export strategy.yaml --format csv
+
+# Compare strategies
+planfile compare old.yaml new.yaml
+
+# Health check
+planfile health .
+```
+
+### Python API
+```python
+from planfile import Strategy
+from planfile.analysis.generator import generator
+
+# Generate from analysis
+strategy = generator.generate_from_current_project(".")
+
+# Create template
+from planfile.cli.extra_commands import generate_template
+template = generate_template("web", "ecommerce")
+
+# Load and analyze
+s = Strategy.load("strategy.yaml")
+stats = s.get_stats()
+
+# Compare
+comparison = s1.compare(s2)
+
+# Export
+yaml_data = s.export("yaml")
+json_data = s.export("json")
+```
+
+### Example Files Generated
+
+Each example folder generates its own set of files:
+
+**quick-start/**
+- `quick-start.yaml` - Basic generated strategy
+- `web-template.yaml` - Web project template
+- `web-template.json` - Template in JSON format
+
+**integrated-functionality/**
+- `generated-from-examples.yaml` - Strategy from file analysis
+- `template-*.yaml` - Project templates (web, mobile, ml)
+- `strategy-export.*` - Various export formats
+- `merged-strategy.yaml` - Combined strategy
+
+**cli-commands/**
+- `cli-example-*.yaml` - Generated strategies
+- `cli-example-*.json` - JSON exports
+- `cli-example.html` - HTML report
+
+**external-tools/**
+- `*.toon.yaml` - External tool outputs (if tools installed)
+- `external-tools-generated.yaml` - Strategy from external analysis
+- `quality-focused.yaml` - Quality-focused strategy
+
+**advanced-usage/**
+- `custom-patterns-strategy.yaml` - Custom analysis strategy
+- `focus-*-strategy.yaml` - Focus-specific strategies
+- `iterative-*.yaml` - Strategy versions
+- `batch-*-strategy.yaml` - Batch processing results
+- `ci-workflow.sh` - Generated CI/CD script
+
+## Tips
+1. Start with `cd quick-start && ./run.sh` for basics
+2. Use `cd integrated-functionality && ./run.sh` for complete overview
+3. Install external tools for deeper analysis: `pip install code2llm vallm redup`
+4. Each example has its own README with detailed information
+5. Check generated YAML files to understand structure
+6. Use `./run.sh` in each folder for easy execution
+
 ```yaml
 project:
   name: "my-project"