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Complete project cleanup and add comprehensive documentation
This commit completes the project restructuring with: ## Cleanup - Remove legacy cpp/ directory (fully migrated to include/ and src/cpp/) - Update CMakeLists.txt to remove legacy paths - Clean up .gitignore (modern, organized) - Add .gitattributes (language detection, line endings) - Update MANIFEST.in (remove legacy references) ## GitHub Integration - Add bug report template (.github/ISSUE_TEMPLATE/bug_report.yml) - Add feature request template (.github/ISSUE_TEMPLATE/feature_request.yml) - Add PR template (.github/PULL_REQUEST_TEMPLATE.md) - All templates follow modern YAML format with validation ## Directory Documentation - Add include/README.md - C++ public headers guide - Add src/cpp/README.md - C++ implementation guide - Add src/python_prtree/README.md - Python package guide - Add tests/README.md - Test suite organization - Each README explains structure, responsibilities, and contribution guidelines ## Migration Documentation - Add MIGRATION.md - Complete migration guide for v0.7.0 - Documents all structural changes - Provides troubleshooting steps - 100% backwards compatible for users - Clear migration path for contributors ## Benefits ### For New Contributors - Every directory has a README explaining its purpose - Clear guidelines on where to add code - GitHub templates guide issue/PR creation - Complete migration guide for existing contributors ### For Project Quality - Clean git history (proper .gitattributes) - Organized .gitignore (no more stray build files) - Professional GitHub templates - Comprehensive documentation at every level ### For Maintainers - Legacy code removed (single source of truth) - Clear contribution path reduces review time - Documentation reduces repetitive questions - Professional appearance attracts contributors ## Documentation Hierarchy ``` Project Root ├── README.md - User-facing documentation ├── ARCHITECTURE.md - System architecture ├── DEVELOPMENT.md - Development setup ├── CONTRIBUTING.md - Contribution guide ├── MIGRATION.md - Migration guide (new) ├── CHANGES.md - Changelog │ ├── include/README.md - C++ headers guide (new) ├── src/cpp/README.md - C++ impl guide (new) ├── src/python_prtree/README.md - Python pkg guide (new) └── tests/README.md - Test suite guide (new) ``` ## Next Steps Ready for prtree.h modularization (1617 lines → separate files).
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‎.gitattributes‎

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# Auto detect text files and perform LF normalization
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* text=auto
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# Source code
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*.cc text
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*.h text
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*.py text
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*.md text
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*.txt text
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*.toml text
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*.yml text
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*.yaml text
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*.json text
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*.cmake text
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*.in text
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# Scripts
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*.sh text eol=lf
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*.bash text eol=lf
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# Documentation
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*.rst text
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*.ipynb text
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# Binary files
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*.so binary
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*.pyd binary
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*.dylib binary
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*.dll binary
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*.a binary
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*.o binary
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*.png binary
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*.jpg binary
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*.jpeg binary
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*.gif binary
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*.ico binary
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*.pdf binary
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# Git
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.gitattributes export-ignore
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.gitignore export-ignore
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.github export-ignore
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# Language statistics for GitHub
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*.h linguist-language=C++
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*.cc linguist-language=C++
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include/prtree/** linguist-language=C++
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src/cpp/** linguist-language=C++
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benchmarks/cpp/** linguist-language=C++

‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug Report
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description: Report a bug or unexpected behavior
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title: "[Bug]: "
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labels: ["bug", "needs-triage"]
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body:
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- type: markdown
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attributes:
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value: |
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Thanks for taking the time to report a bug! Please fill out the information below.
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- type: textarea
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id: description
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attributes:
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label: Bug Description
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description: A clear and concise description of what the bug is.
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placeholder: Describe the bug...
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validations:
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required: true
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- type: textarea
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id: reproduce
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attributes:
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label: Steps to Reproduce
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description: Steps to reproduce the behavior
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placeholder: |
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1. Create a tree with...
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2. Call query with...
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3. See error...
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validations:
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required: true
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- type: textarea
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id: expected
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attributes:
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label: Expected Behavior
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description: What did you expect to happen?
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placeholder: Expected to return...
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validations:
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required: true
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- type: textarea
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id: actual
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attributes:
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label: Actual Behavior
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description: What actually happened? Include any error messages.
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placeholder: |
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Error message:
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```
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paste error here
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```
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validations:
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required: true
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- type: textarea
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id: code
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attributes:
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label: Minimal Reproducible Example
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description: Please provide a minimal code example that reproduces the issue
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placeholder: |
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```python
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from python_prtree import PRTree2D
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# your code here
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```
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render: python
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validations:
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required: true
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- type: input
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id: version
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attributes:
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label: python_prtree Version
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description: What version are you using?
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placeholder: "0.7.0"
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validations:
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required: true
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- type: input
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id: python-version
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attributes:
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label: Python Version
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description: What Python version are you using?
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placeholder: "3.11"
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validations:
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required: true
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- type: dropdown
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id: os
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attributes:
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label: Operating System
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options:
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- Linux
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- macOS
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- Windows
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- Other
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validations:
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required: true
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- type: textarea
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id: additional
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attributes:
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label: Additional Context
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description: Add any other context about the problem here
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placeholder: Any additional information...

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: Feature Request
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description: Suggest a new feature or enhancement
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title: "[Feature]: "
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labels: ["enhancement"]
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body:
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- type: markdown
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attributes:
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value: |
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Thanks for suggesting a feature! Please fill out the information below.
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- type: textarea
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id: problem
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attributes:
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label: Problem Statement
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description: Is your feature request related to a problem? Please describe.
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placeholder: I'm always frustrated when...
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validations:
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required: true
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- type: textarea
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id: solution
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attributes:
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label: Proposed Solution
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description: Describe the solution you'd like
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placeholder: I would like to be able to...
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validations:
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required: true
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- type: textarea
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id: alternatives
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attributes:
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label: Alternatives Considered
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description: Describe alternatives you've considered
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placeholder: I've considered...
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- type: textarea
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id: example
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attributes:
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label: Example Usage
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description: How would you use this feature?
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placeholder: |
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```python
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# Example code showing desired API
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tree.new_feature(...)
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```
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render: python
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- type: checkboxes
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id: contribution
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attributes:
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label: Contribution
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description: Would you be willing to contribute this feature?
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options:
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- label: I'm willing to submit a PR for this feature

‎.github/PULL_REQUEST_TEMPLATE.md‎

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## Description
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<!-- Please include a summary of the changes and the related issue. -->
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Fixes #(issue)
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## Type of Change
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<!-- Please check the one that applies to this PR -->
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- [ ] Bug fix (non-breaking change which fixes an issue)
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- [ ] New feature (non-breaking change which adds functionality)
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- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
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- [ ] Documentation update
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- [ ] Code refactoring
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- [ ] Performance improvement
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- [ ] Test addition or modification
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## Changes Made
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<!-- List the main changes in this PR -->
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-
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-
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-
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## Testing
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<!-- Describe the tests that you ran to verify your changes -->
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- [ ] All existing tests pass (`make test` or `pytest`)
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- [ ] Added new tests for new functionality
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- [ ] Tested on multiple Python versions (if applicable)
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- [ ] Tested on multiple platforms (if applicable)
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### Test Commands Run
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```bash
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# List the test commands you ran
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make test
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pytest tests/unit/test_*.py -v
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```
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## Documentation
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- [ ] Updated docstrings for modified functions/classes
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- [ ] Updated README.md (if needed)
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- [ ] Updated CHANGES.md
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- [ ] Updated type hints (if applicable)
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## Checklist
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- [ ] My code follows the project's code style (`make format` and `make lint` pass)
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- [ ] I have performed a self-review of my code
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- [ ] I have commented my code, particularly in hard-to-understand areas
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- [ ] My changes generate no new warnings
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- [ ] I have added tests that prove my fix is effective or that my feature works
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- [ ] New and existing unit tests pass locally with my changes
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- [ ] Any dependent changes have been merged and published
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## Performance Impact
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<!-- If applicable, describe any performance implications -->
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- [ ] No performance impact
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- [ ] Performance improvement (describe below)
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- [ ] Potential performance regression (describe below and justify)
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## Breaking Changes
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<!-- If this is a breaking change, describe the impact and migration path -->
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N/A
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## Additional Notes
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<!-- Any additional information that reviewers should know -->

‎.gitignore‎

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cmake-build-*/
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docker/
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ldata/
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# Build artifacts
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build/
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build_*/
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dist/
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_build/
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_generate/
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*.egg-info/
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*.so
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*.so.*
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*.pyd
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*.dylib
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*.dll
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*.a
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*.py[cod]
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*.egg-info
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.eggs/
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.idea/
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input/*
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!input/.gitkeep
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*.o
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# Python
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__pycache__/
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.ipynb_checkpoints/
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*.py[cod]
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*$py.class
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*.egg
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.Python
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.pytest_cache/
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.coverage
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htmlcov/
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.tox/
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.nox/
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.hypothesis/
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.mypy_cache/
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.dmypy.json
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dmypy.json
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.ruff_cache/
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# IDEs
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.vscode/
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.idea/
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*.swp
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*.swo
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*~
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.DS_Store
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*.prof
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# Test coverage
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htmlcov/
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.coverage
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.coverage.*
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coverage.xml
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*.cover
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# Pytest
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.pytest_cache/
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.pytest_cache
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# CMake
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CMakeCache.txt
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CMakeFiles/
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cmake_install.cmake
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Makefile
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compile_commands.json
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# Build artifacts
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*.o
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*.obj
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*.lib
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*.exp
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# Profiling
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*.prof
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*.log
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callgrind.*
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perf.data*
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# Temporary files
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*.tmp
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*.bak
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*~
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# Documentation
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docs/_build/
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site/
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# Phase 0 profiling artifacts (keep templates, ignore generated data)
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docs/baseline/reports/*.txt
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docs/baseline/reports/*.out
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docs/baseline/reports/*.data
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docs/baseline/flamegraphs/*.svg
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*_benchmark_results.csv
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*.prof
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perf.data
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perf.data.old
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cachegrind.out*
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# Local development
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.env
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.venv
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venv/
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ENV/
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env/

‎CMakeLists.txt‎

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# Include directories
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set(PRTREE_INCLUDE_DIRS
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${CMAKE_CURRENT_SOURCE_DIR}/include
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${CMAKE_CURRENT_SOURCE_DIR}/cpp # Backward compatibility during migration
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)
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option(SNAPPY_BUILD_TESTS "" OFF)

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