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joshfactorialjoshfactorial
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Merge pull request #284 from ncsa/develop
Updating version and changelog, adding GC Bias modeling
2 parents f3268ed + e55d344 commit 349f9ca

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‎.gitattributes‎

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models/* linguist-generated
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# Set default behavior, in case people don't have core.autocrlf set.
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* text=auto
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*.py text
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*.yml text
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*.fa text
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*.fasta text
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*.vcf text
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*.fastq text
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*.txt text
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*.html text
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*.genomecov text
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*.bam binary
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*.png binary
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*.jpg binary
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models/* linguist-generated
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# Set default behavior, in case people don't have core.autocrlf set.
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* text=auto
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*.py text
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*.yml text
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*.fa text
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*.fasta text
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*.vcf text
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*.fastq text
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*.txt text
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*.html text
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*.genomecov text
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*.bam binary
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*.png binary
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*.jpg binary

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Browser [e.g. chrome, safari]
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- Version [e.g. 22]
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Browser [e.g. stock browser, safari]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.
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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. iOS]
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- Browser [e.g. chrome, safari]
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- Version [e.g. 22]
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**Smartphone (please complete the following information):**
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- Device: [e.g. iPhone6]
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- OS: [e.g. iOS8.1]
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- Browser [e.g. stock browser, safari]
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- Version [e.g. 22]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.
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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/workflows/python-app.yml‎

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- name: Run unit tests
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shell: bash -l {0}
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run: |
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micromamba run -n neat pytest -q tests
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micromamba run -n neat pytest --cov=neat --cov-report=xml --cov-report=term tests
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- name: Run CLI integration test
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shell: bash -l {0}
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run: |
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micromamba run -n neat pytest -q tests/test_cli
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v4
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with:
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file: ./coverage.xml
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fail_ci_if_error: false

‎.gitignore‎

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# Ignore filetypes
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*.pyc
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*.pyo
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*.pyd
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__pycache__/
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# Virtual environments
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/python2env/
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/.venv/
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/venv/
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/env/
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# IDEs
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/.ipynb_checkpoints/
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/.vscode/
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/.idea/
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# Test & coverage artifacts
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.coverage
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.coverage.*
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htmlcov/
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.pytest_cache/
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# NEAT log files
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*.log
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# Build / packaging
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dist/
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build/
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*.egg-info/
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*.egg
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# Ignore filetypes
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*.pyc
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*.pyo
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*.pyd
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__pycache__/
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# Virtual environments
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/python2env/
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/.venv/
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/venv/
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/env/
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# IDEs
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/.ipynb_checkpoints/
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/.vscode/
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/.idea/
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# Test & coverage artifacts
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.coverage
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.coverage.*
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htmlcov/
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.pytest_cache/
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# NEAT log files
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*.log
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# Build / packaging
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dist/
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build/
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*.egg-info/
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*.egg
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# gitnexus stuff
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/.gitnexus/
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/.claude/
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AGENTS.md
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CLAUDE.md

‎AGENTS.md‎

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<!-- gitnexus:start -->
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# GitNexus — Code Intelligence
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This project is indexed by GitNexus as **NEAT** (2742 symbols, 5450 relationships, 62 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
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> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
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## Always Do
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- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
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- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
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- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
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- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
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- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
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## Never Do
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- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
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- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
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- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
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- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
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## Resources
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| Resource | Use for |
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|----------|---------|
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| `gitnexus://repo/NEAT/context` | Codebase overview, check index freshness |
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| `gitnexus://repo/NEAT/clusters` | All functional areas |
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| `gitnexus://repo/NEAT/processes` | All execution flows |
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| `gitnexus://repo/NEAT/process/{name}` | Step-by-step execution trace |
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## CLI
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| Task | Read this skill file |
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|------|---------------------|
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| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
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| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
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| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
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| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
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| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
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| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
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<!-- gitnexus:end -->

‎CLAUDE.md‎

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<!-- gitnexus:start -->
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# GitNexus — Code Intelligence
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This project is indexed by GitNexus as **NEAT** (2742 symbols, 5450 relationships, 62 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.
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> If any GitNexus tool warns the index is stale, run `npx gitnexus analyze` in terminal first.
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## Always Do
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- **MUST run impact analysis before editing any symbol.** Before modifying a function, class, or method, run `gitnexus_impact({target: "symbolName", direction: "upstream"})` and report the blast radius (direct callers, affected processes, risk level) to the user.
11+
- **MUST run `gitnexus_detect_changes()` before committing** to verify your changes only affect expected symbols and execution flows.
12+
- **MUST warn the user** if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
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- When exploring unfamiliar code, use `gitnexus_query({query: "concept"})` to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
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- When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use `gitnexus_context({name: "symbolName"})`.
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## Never Do
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- NEVER edit a function, class, or method without first running `gitnexus_impact` on it.
19+
- NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
20+
- NEVER rename symbols with find-and-replace — use `gitnexus_rename` which understands the call graph.
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- NEVER commit changes without running `gitnexus_detect_changes()` to check affected scope.
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## Resources
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| Resource | Use for |
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|----------|---------|
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| `gitnexus://repo/NEAT/context` | Codebase overview, check index freshness |
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| `gitnexus://repo/NEAT/clusters` | All functional areas |
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| `gitnexus://repo/NEAT/processes` | All execution flows |
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| `gitnexus://repo/NEAT/process/{name}` | Step-by-step execution trace |
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## CLI
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| Task | Read this skill file |
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|------|---------------------|
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| Understand architecture / "How does X work?" | `.claude/skills/gitnexus/gitnexus-exploring/SKILL.md` |
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| Blast radius / "What breaks if I change X?" | `.claude/skills/gitnexus/gitnexus-impact-analysis/SKILL.md` |
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| Trace bugs / "Why is X failing?" | `.claude/skills/gitnexus/gitnexus-debugging/SKILL.md` |
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| Rename / extract / split / refactor | `.claude/skills/gitnexus/gitnexus-refactoring/SKILL.md` |
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| Tools, resources, schema reference | `.claude/skills/gitnexus/gitnexus-guide/SKILL.md` |
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| Index, status, clean, wiki CLI commands | `.claude/skills/gitnexus/gitnexus-cli/SKILL.md` |
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<!-- gitnexus:end -->

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