fix: resolve security vulnerabilities, file downloads, Docker build, and Windows script compatibility

[AnandkumarMall]

Summary / 概述

This PR comprehensively resolves multiple reported community issues and security vulnerabilities across backend APIs, file downloads, Docker builds, Windows scripts, and citation parsing.

本 PR 全面修复了社区反馈的安全漏洞、文件下载缺失、Docker 镜像构建中断、Windows 脚本兼容性及参考文献解析问题。

Fixes #60, fixes #61, fixes #62, fixes #64, fixes #65, fixes #73, fixes #83, fixes #86, fixes #87, fixes #88, fixes #89, fixes #90, fixes #95, fixes #100, fixes #110, fixes #114, fixes #118, fixes #120.

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1. Security & Path Traversal / 安全与防路径遍历

• CORS Fix: Replaced allow_origins=["*"] with allow_origin_regex=r".*" when allow_credentials=True in backend/app/main.py. This complies with the CORS specification and prevents browsers from blocking requests with credentials (bug :Invalid and unsafe CORS configuration (allow_origins=["*"] with allow_credentials=True) #90).
• Path Traversal Protection: Hardened get_work_dir and create_work_dir in backend/app/utils/common_utils.py using ensure_safe_task_id and directory containment checks against ../../ traversal (bug : Path traversal in /files and /open_folder because task_id is not validated #88).
• File Upload Sanitization: Extracted safe basename for uploaded files in /modeling and blocked writing outside the task directory (bug: Path traversal in /modeling file upload via unsanitized UploadFile.filename #87).
• File Download Hardening: Added safe filename validation in /download_url preventing arbitrary file access (issue: Generated task artifacts and task message logs are exposed without authentication #89).
• Base URL Normalization: Automatically trimmed trailing /chat/completions and trailing slashes from API Base URLs during validation and saving (bug : Unauthenticated /save-api-config mutates process-global API settings and breaks multi-user isolation #86).

2. File Operations & Broken Downloads / 文件管理与下载修复

• Zip Download 404 Fix: /download_all_url previously pointed to /static/{task_id}/all.zip which was never created. Added dynamic on-demand zip archiving of the task workspace (文件方面的操作均无法实现。只能手动复制路径去文件资源管理器里看 #110).
• Dynamic Host: Changed /download_url from hardcoded localhost:8000 to settings.SERVER_HOST.
• Folder Explorer Fix: Converted relative path to absolute path (os.path.abspath) for Windows explorer, and added cross-platform fallbacks for Linux (xdg-open) and macOS (open).

3. Docker & Deployment / 容器构建与历史记录

• pnpm Version Pin: Pinned RUN npm install -g pnpm@10.6.3 in frontend/Dockerfile matching packageManager in package.json, resolving ERR_PNPM_PNPM_ENGINE_IDENTITY_UNVERIFIABLE (Docker 部署 frontend 构建失败：pnpm 新版本与旧 lockfile 不兼容 #118, Docker 部署报错 #83).
• Chat History Persistence: Added ./backend/logs:/app/logs volume mounting to docker-compose.yml so chat history is preserved across container restarts (docker部署版MMA重新启动时会丢失所有历史记录 #64).
• UTF-8 Locale: Injected ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 into backend/Dockerfile (docker不支持中文 #60).

4. Windows Scripts & Quality Gates / Windows 脚本与环境兼容

• Virtualenv & Pre-flight Checks: Updated win_start.bat to detect both backend\venv and backend\.venv (generated by uv sync), and added checks for redis-server and pnpm (fix: win_start.bat 兼容 .venv 并增加启动前置检查 #116).
• Interpreter Detection: Updated writing_check.sh and doctor/SKILL.md to automatically detect Windows native python when python3 is absent (Windows 下 6verity 验收与 doctor 环境检测因 python3 硬编码而失效 #114, fix(skills): Windows 下 python3 硬编码导致 6verity/doctor 失效 #115).
• Option Parser Loop Fix: Fixed infinite loop when arguments are missing values in writing_check.sh.
• Doctor Fallback Return Code: Added explicit return 0 / return 1 codes in doctor/SKILL.md so the fallback chain works properly.

5. Citations & Typst Math / 参考文献与 Typst 语法

• Reference Extraction: Updated the regex in user_output.py to make colons optional ((?::|\s)\s*), aligning with the writer prompt ({[^1] ...}) (fix: 修复参考文献收集失败、编号错乱与标题/条目格式问题 #113).
• Citation Deduplication: Corrected repeated citations across sections to reuse original reference numbers.
• Typst LaTeX Leak Protection: Added a Typst math symbol reference table in 5writing/SKILL.md and added automated static scanning in writing_check.sh to flag leaked LaTeX macros (\text{}, \times, \degree, etc.) in .typ files (Claude Code使用skill用Typst引擎语法还会有latex语法残留 #100).

6. Observability & Usability / 交互与可观测性

• Live Chat Turn Progress: Added real-time chat turn progress updates (SystemMessage) pushed to the frontend on each coder agent turn (希望能够添加聊天次数的实时显示 #65).
• Error Visibility: Pushed formatted warnings to the UI upon coder execution exceptions rather than silently getting stuck (建议加个报错处理 #73).
• Decoupled Optional Services: Removed the hard assertion requiring OPENALEX_EMAIL in workflow.py (MathModel-Skill 的恢复机制会触发已被禁用的 thread/rollback #120).
• Model Selection Flexibility: Allowed custom model choices in skills prompt (建议在最初的模型选型增加“其它”用户可编辑的选项 #95).
• Documentation: Fixed broken anchor links in README.md, corrected the sponsor path (./docs/md/sponser.md), and added configuration guides for MAX_CHAT_TURNS, MAX_RETRIES, and API Base URLs (readme.md缺少配置教程 #61, 建议在README.md里添加如何修改最大聊天次数的教程 #62, docs: 修正 README 中失效的目录锚点与文档路径 #122).

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Verification / 验证

• Unit Tests: Added backend/app/tests/test_user_output.py covering citation collection, reference numbering, path safety, and URL normalization. All 7 tests pass (Ran 7 tests in 0.004s - OK).
• Code Style: ruff check app/ passed with 0 errors.