deep_research/README.md

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

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/:

./setup.sh init all

Initialize one platform:

./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:

./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.