Add current codebase for retroactive review

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: 🐛 Bug Report
+about: Report a bug to help us improve the project
+title: '[BUG] '
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Description
+
+<!-- A clear and concise description of what the bug is -->
+
+## Steps to Reproduce
+
+1.
+2.
+3.
+
+**Code snippet (if applicable):**
+```python
+# Your code here
+```
+
+## Expected Behavior
+
+<!-- A clear description of what you expected to happen -->
+
+## Actual Behavior
+
+<!-- A clear description of what actually happened -->
+
+## Environment
+
+- **Component:** [API | Core functionality | Any]
+- **OS:** [Windows | MacOS | Linux]
+- **Python Version:**
+
+## Screenshots/Logs
+
+<!-- If applicable, add screenshots or error logs -->
+
+## Additional Context
+
+<!-- Add any other context about the problem here -->
+
+## Possible Solution
+
+<!-- If you have suggestions on how to fix the bug, please describe them here -->

.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: 💬 Discussion
+    url: https://github.com/VectorInstitute/aieng-template-uv/discussions
+    about: Ask questions or discuss ideas with the community
+  - name: 📖 Documentation
+    url: https://github.com/VectorInstitute/aieng-template-uv#readme
+    about: Check the documentation for setup and usage guides

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: ✨ Feature Request
+about: Suggest a new feature or enhancement
+title: '[FEATURE] '
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Problem Statement
+
+<!-- Is your feature request related to a problem? Describe the problem or use case -->
+
+## Proposed Solution
+
+<!-- A clear description of what you want to happen -->
+
+## Alternative Solutions
+
+<!-- Describe any alternative solutions or features you've considered -->
+
+## Use Cases
+
+<!-- Describe specific use cases where this feature would be valuable -->
+-
+-
+-
+
+## Implementation Ideas
+
+<!-- If you have ideas about how this could be implemented, describe them here -->
+
+## Component Impact
+
+<!-- Which parts of the system would this feature affect? -->
+- [ ] API
+- [ ] Core functionality
+- [ ] Docker/Infrastructure
+- [ ] Documentation
+- [ ] Any other part of the system
+
+## Additional Context
+
+<!-- Add any other context, mockups, or screenshots about the feature request here -->
+
+## Priority
+
+<!-- How important is this feature to you? -->
+- [ ] Nice to have
+- [ ] Would be helpful
+- [ ] Important for my use case
+- [ ] Critical/blocking

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "daily"
+
+  # Keep uv dependencies (uv.lock) up to date
+  - package-ecosystem: "uv"
+    directory: "/"          # where pyproject.toml and uv.lock live
+    schedule:
+      interval: "daily"

.github/pull_request_template.md

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+## Summary
+
+<!-- Provide a brief description of what this PR does -->
+
+Clickup Ticket(s): Link(s) if applicable.
+
+## Type of Change
+
+- [ ] 🐛 Bug fix (non-breaking change that fixes an issue)
+- [ ] ✨ New feature (non-breaking change that adds functionality)
+- [ ] 💥 Breaking change (fix or feature that would cause existing functionality to not work as expected)
+- [ ] 📝 Documentation update
+- [ ] 🔧 Refactoring (no functional changes)
+- [ ] ⚡ Performance improvement
+- [ ] 🧪 Test improvements
+- [ ] 🔒 Security fix
+
+## Changes Made
+
+<!-- List the main changes made in this PR -->
+-
+-
+-
+
+## Testing
+
+<!-- Describe how you tested these changes -->
+- [ ] Tests pass locally (`uv run pytest tests/`)
+- [ ] Type checking passes (`uv run mypy <src_dir>`)
+- [ ] Linting passes (`uv run ruff check src_dir/`)
+- [ ] Manual testing performed (describe below)
+
+**Manual testing details:**
+<!-- Describe any manual testing performed -->
+
+## Screenshots/Recordings
+
+<!-- If applicable, add screenshots or recordings to demonstrate the changes -->
+
+## Related Issues
+
+<!-- Link any related issues using "Closes #123" or "Relates to #123" -->
+
+## Deployment Notes
+
+<!-- Any special deployment considerations or migration steps -->
+
+## Checklist
+
+- [ ] Code follows the project's style guidelines
+- [ ] Self-review of code completed
+- [ ] Documentation updated (if applicable)
+- [ ] No sensitive information (API keys, credentials) exposed

.github/workflows/code_checks.yml

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+name: code checks
+permissions:
+  contents: read
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+      - '**.ipynb'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/code_checks.yml
+      - '**.py'
+      - uv.lock
+      - pyproject.toml
+      - '**.ipynb'
+
+jobs:
+  run-code-check:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.3.0
+        with:
+          # Install a specific version of uv.
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: "Set up Python"
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Install dependencies and check code
+        run: |
+          source .venv/bin/activate
+          pre-commit run --all-files
+
+      - name: Install pip in venv (for pip-audit)
+        run: uv pip install pip
+
+      - name: pip-audit (gh-action-pip-audit)
+        uses: pypa/gh-action-pip-audit@v1.1.0
+        with:
+          virtual-environment: .venv/
+          ignore-vulns: |
+            GHSA-4xh5-x5gv-qwph
+            CVE-2025-69872
+            CVE-2026-28277
+            CVE-2026-32597
+            CVE-2026-25960
+            CVE-2026-25048

.github/workflows/docs.yml

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+name: docs
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.html'
+      - '**.js'
+      - '**.md'
+      - uv.lock
+      - pyproject.toml
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - .pre-commit-config.yaml
+      - .github/workflows/docs.yml
+      - '**.py'
+      - '**.ipynb'
+      - '**.js'
+      - '**.html'
+      - uv.lock
+      - pyproject.toml
+      - '**.md'
+      - mkdocs.yml
+      - '**.png'
+      - '**.svg'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7.3.0
+        with:
+          version: "0.9.11"
+          enable-cache: true
+
+      - name: Set up Python
+        uses: actions/setup-python@v6.2.0
+        with:
+          python-version-file: ".python-version"
+
+      - name: Install the project
+        run: uv sync --extra docs
+
+      - name: Build docs
+        run: uv run mkdocs build
+        env:
+          PYTHONPATH: src
+
+      - name: Create .nojekyll file
+        run: touch site/.nojekyll
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v6
+        with:
+          name: docs-site
+          path: site/
+          retention-days: 1
+
+  deploy:
+    needs: build
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v6.0.2
+
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+
+      - name: Download artifact
+        uses: actions/download-artifact@v7
+        with:
+          name: docs-site
+          path: site
+
+      - name: Ensure .nojekyll exists
+        run: touch site/.nojekyll
+
+      - name: Deploy to Github pages
+        uses: JamesIves/github-pages-deploy-action@v4.8.0
+        with:
+          branch: gh-pages
+          folder: site