# Deep Research

生物医药 Deep Research 仓库。根目录只保留入口说明和环境重建脚本；所有源文件放在 `src/`，各平台运行目录由脚本生成。

## Directory Layout

```text
deep_research/
  README.md
  setup.sh
  src/                  # canonical source: scripts, skills, docs, configs, platform adapters
  codex/                # generated Codex workspace
  antigravity/          # generated Antigravity workspace
  opencode/             # generated OpenCode workspace
  claude-code/          # generated Claude Code workspace
  gemini-cli/           # generated Gemini CLI workspace
```

Generated platform directories are ignored by Git. Rebuild them whenever source templates change.

## Setup

Initialize all platform workspaces from local `src/`:

```bash
./setup.sh init all
```

Initialize one platform:

```bash
./setup.sh init antigravity
./setup.sh init codex
./setup.sh init opencode
./setup.sh init claude-code
./setup.sh init gemini-cli
```

Pull latest changes and rebuild:

```bash
./setup.sh update all
./setup.sh update antigravity
```

After rebuilding, open the generated platform directory in the matching tool:

- Codex: `deep_research/codex`
- Antigravity: `deep_research/antigravity`
- OpenCode: `deep_research/opencode`
- Claude Code: `deep_research/claude-code`
- Gemini CLI: `deep_research/gemini-cli`

## Source

Shared skills and research rules should live in `src/` and be reused by platform adapters. Avoid duplicating method, source-quality, citation, evidence, and output-hygiene rules inside platform-specific files unless the platform requires a thin wrapper.

Key source locations:

- `src/scripts/`
- `src/configs/`
- `src/skills/`
- `src/platform_adapters/`
- `src/docs/`
- `src/PLAN.md`

Platform-specific behavior is documented in each generated workspace README and in `src/docs/platform-branch-strategy.md`.