Imported from gdmuna/TalosArk (AGENTS.md). Install upstream with npx skills add gdmuna/TalosArk. Copyright stays with the author.

项目定位

生物样本储存管理系统 monorepo，包含三个工作区：

• apps/backend — NestJS 后端服务
• apps/docsite — VitePress 文档站
• apps/frontend — Vue 3 前端

文档导航

以下文档按需加载。仅在对应场景触发时才去读取，减少不必要的上下文占用。

硬性约束

以下是工具链与安全层面的操作底线。

• 包管理：只用 pnpm，禁止 npm/yarn
• 后端架构分层：Controller → Service → Repository（Prisma）
• 前端架构分层：Page → Store（Pinia）→ API（Alova）；状态不绕过 store 直接写
• 依赖注入：优先使用构造函数注入与控制反转，除非迫不得已才手动 new
• 提交规范：<type>(<scope>): <subject>（Conventional Commits）
• 禁止绕过 Git 钩子（--no-verify）
• 禁止硬编码敏感信息，不假设 .env 文件存在
• 前端 shadcn-vue 组件（src/components/ui/）禁止直接手改，通过 shadcn skill 管理

常用命令速查

# monorepo 根
pnpm run format          # Prettier 格式化（全工作区）
pnpm run format:check    # 格式检查

# 后端 service
pnpm --filter @talos-ark/backend start:dev      # 热重载开发
pnpm --filter @talos-ark/backend build          # 编译 + 类型检查
pnpm --filter @talos-ark/backend test           # 单元测试 + E2E
pnpm --filter @talos-ark/backend lint:fix       # ESLint 自动修复
pnpm --filter @talos-ark/backend db:migrate     # 数据库迁移
pnpm --filter @talos-ark/backend db:gen-client  # 重新生成 Prisma Client

# 前端
pnpm --filter @talos-ark/frontend dev           # 启动开发服务器（:8081）
pnpm --filter @talos-ark/frontend type-check    # vue-tsc 类型检查
pnpm --filter @talos-ark/frontend test          # Vitest 单元测试
pnpm --filter @talos-ark/frontend test:e2e      # Playwright E2E 测试
pnpm --filter @talos-ark/frontend build         # 构建产物
pnpm --filter @talos-ark/frontend eslint        # ESLint 自动修复

GitNexus — Code Intelligence

This project is indexed by GitNexus as biological-storage-box (2108 symbols, 3398 relationships, 62 execution flows). Use the GitNexus MCP tools to understand code, assess impact, and navigate safely.

If any GitNexus tool warns the index is stale, run npx gitnexus analyze in terminal first.

Always Do

• 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.
• MUST run gitnexus_detect_changes() before committing to verify your changes only affect expected symbols and execution flows.
• MUST warn the user if impact analysis returns HIGH or CRITICAL risk before proceeding with edits.
• When exploring unfamiliar code, use gitnexus_query({query: "concept"}) to find execution flows instead of grepping. It returns process-grouped results ranked by relevance.
• When you need full context on a specific symbol — callers, callees, which execution flows it participates in — use gitnexus_context({name: "symbolName"}).

When Debugging

1. gitnexus_query({query: "<error or symptom>"}) — find execution flows related to the issue
2. gitnexus_context({name: "<suspect function>"}) — see all callers, callees, and process participation
3. READ gitnexus://repo/biological-storage-box/process/{processName} — trace the full execution flow step by step
4. For regressions: gitnexus_detect_changes({scope: "compare", base_ref: "main"}) — see what your branch changed

When Refactoring

• Renaming: MUST use gitnexus_rename({symbol_name: "old", new_name: "new", dry_run: true}) first. Review the preview — graph edits are safe, text_search edits need manual review. Then run with dry_run: false.
• Extracting/Splitting: MUST run gitnexus_context({name: "target"}) to see all incoming/outgoing refs, then gitnexus_impact({target: "target", direction: "upstream"}) to find all external callers before moving code.
• After any refactor: run gitnexus_detect_changes({scope: "all"}) to verify only expected files changed.

Never Do

• NEVER edit a function, class, or method without first running gitnexus_impact on it.
• NEVER ignore HIGH or CRITICAL risk warnings from impact analysis.
• NEVER rename symbols with find-and-replace — use gitnexus_rename which understands the call graph.
• NEVER commit changes without running gitnexus_detect_changes() to check affected scope.

Tools Quick Reference

Impact Risk Levels

Resources

Self-Check Before Finishing

Before completing any code modification task, verify:

1. gitnexus_impact was run for all modified symbols
2. No HIGH/CRITICAL risk warnings were ignored
3. gitnexus_detect_changes() confirms changes match expected scope
4. All d=1 (WILL BREAK) dependents were updated

Keeping the Index Fresh

After committing code changes, the GitNexus index becomes stale. Re-run analyze to update it:

npx gitnexus analyze

If the index previously included embeddings, preserve them by adding --embeddings:

npx gitnexus analyze --embeddings

To check whether embeddings exist, inspect .gitnexus/meta.json — the stats.embeddings field shows the count (0 means no embeddings). Running analyze without --embeddings will delete any previously generated embeddings.

Claude Code users: A PostToolUse hook handles this automatically after git commit and git merge.

CLI

Project Planning & Progress

PROGRESS.md is mandatory reading before implementing any ROADMAP item. It defines which files to create, which tests to write, and the exact commands that must all pass before a feature is considered done.