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fix: harden analysis API and polish repository
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‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: Bug report
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description: Report a reproducible problem in PureAutoCodeQL.
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title: "bug: "
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labels:
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- bug
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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 this. Please remove secrets and private target details before submitting.
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- type: textarea
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id: summary
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attributes:
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label: Summary
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description: What went wrong?
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placeholder: The analysis fails when...
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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: Reproduction steps
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description: Include commands, case layout, and relevant configuration.
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placeholder: |
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1. Run `uv run python Analyze.py ...`
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2. Observe ...
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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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validations:
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required: true
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- type: textarea
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id: logs
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attributes:
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label: Logs or output
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description: Paste the smallest useful snippet. Redact tokens and private paths if needed.
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render: shell
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- type: input
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id: python
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attributes:
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label: Python version
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placeholder: "3.13.x"
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- type: input
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id: codeql
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attributes:
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label: CodeQL CLI version
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placeholder: "`codeql version` output"
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- type: dropdown
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id: language
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attributes:
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label: Target language
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options:
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- Java
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- Python
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- C/C++
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- Other
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- type: textarea
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id: extra
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attributes:
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label: Additional context
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description: Anything else that may help diagnose the issue.

‎.github/ISSUE_TEMPLATE/config.yml‎

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blank_issues_enabled: true
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contact_links:
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- name: Security issue
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url: https://github.com/Fruit-Guardians/PureAutoCodeql/security/policy
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about: Please avoid public exploit details. Review the security policy first.

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: Feature request
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description: Suggest an improvement or new capability.
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title: "feat: "
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labels:
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- enhancement
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body:
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- type: textarea
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id: problem
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attributes:
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label: Problem
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description: What research or workflow problem would this solve?
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placeholder: I need PureAutoCodeQL to...
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validations:
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required: true
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- type: textarea
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id: proposal
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attributes:
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label: Proposed solution
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description: Describe the behavior you want.
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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: Other approaches or workarounds you tried.
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- type: dropdown
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id: area
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attributes:
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label: Area
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options:
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- CLI
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- API
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- CodeQL generation
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- Project import
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- Path selection
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- Configuration
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- Documentation
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- Other
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- type: textarea
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id: context
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attributes:
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label: Additional context
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description: Sample inputs, target languages, or links to related docs.

‎.github/pull_request_template.md‎

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## Summary
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-
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## Validation
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- [ ] `uv run pytest -q`
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- [ ] `uv lock --check`
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- [ ] `git diff --check`
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## Notes
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Describe any skipped checks, follow-up work, or operational impact.

‎.gitignore‎

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*.swp
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*.swo
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*~
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config/keys.toml
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config\\keys.toml
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config/keys*.toml
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config\\keys*.toml
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!config/keys.example.toml
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!config\\keys.example.toml
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# 配置文件 - 敏感信息
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.env
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*.zip
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projects/*.zip
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projects/C_Qi
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utils/lsp
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utils/lsp

‎Analyze.py‎

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使用示例:
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%(prog)s --case CVE-2021-21985 # 分析已导入的案例
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%(prog)s --case "C:\\Targets\\java\\CVE-2023-51444" # Java项目：自动导入+建库+分析
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%(prog)s --case CVE-2021-21985 --stream # 显示AI思考过程
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%(prog)s --case CVE-2021-21985 --no-stream # 禁用AI思考过程显示
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%(prog)s --import-project "C:\\Targets\\CVE-2023-51444" --import-language java # 仅导入Java项目
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%(prog)s --md-file vulnerability.md # 从MD文件直接生成CodeQL
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%(prog)s --md-file vulnerability.md --src-path /path/to/source # 从MD文件生成source点分析报告

‎CONTRIBUTING.md‎

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# Contributing
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Thanks for helping improve PureAutoCodeQL.
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## Development Setup
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```bash
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git clone https://github.com/Fruit-Guardians/PureAutoCodeql.git
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cd PureAutoCodeql
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uv sync
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```
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Build the MCP ripgrep tool when you need agent-side code search:
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```bash
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chmod +x build_mcp.sh
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./build_mcp.sh
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```
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## Before Opening a Pull Request
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Please run the focused checks that match your change. For broad changes, run:
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```bash
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uv run pytest -q
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uv lock --check
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uv run python -m compileall -q Analyze.py api core services utils agents tools
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```
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For documentation-only changes, at minimum check Markdown links and run:
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```bash
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git diff --check
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```
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## Pull Request Guidance
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- Keep the change focused and explain why it is needed.
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- Include reproduction steps for bug fixes.
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- Include sample input or output when behavior changes.
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- Do not commit secrets, generated local reports, or private target projects.
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- Follow existing module boundaries and local coding style.
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## Commit Message Examples
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```text
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fix: harden project import path validation
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feat: add source-sink fallback query mode
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docs: refresh API quickstart
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test: cover unsafe case id rejection
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```

‎LICENSE‎

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MIT License
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Copyright (c) 2026 Fruit Guardians
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

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