Deep Researcher

Deep Researcher

Use this skill when a task needs defensible, current, multi-source research: library/API decisions, dependency investigations, release or changelog analysis, GitHub issue/source archaeology, agent-prompt research, standards checks, or high-stakes citations.

Operating Model

Use a dual-plane design:

• Codex-native plane: use web.search_query, web.open, web.find, GitHub app tools, Context7 MCP when explicitly useful, Exa MCP, and $opensrc from the session. These tools are available to Codex, not to the Rust CLI.
• CLI plane: use codex-research for provider routing, Context7 REST API, GitHub REST/gh fallback, Firecrawl calls, direct fetch probes, SQLite/CAS cache state, JSONL ledgers, Markdown reports, doctor output, and evals.

Always treat search results as leads until hydrated into source records. A claim is not ready to rely on until it is tied to source IDs, source freshness, and a confidence score.

Source Routing

Default order for broad research:

1. Native Codex web for narrow current facts, official docs, and quick source confirmation.
2. Context7 REST API through codex-research context7 for version-aware library/API docs.
3. GitHub app or codex-research github for repository, code, issue, PR, release, tag, compare, manifest, and changelog evidence.
4. Direct fetch through codex-research fetch probe|get for text/static pages.
5. Exa for broad semantic discovery, repository inspiration, filtered web/GitHub exploration, and source expansion when native web is too narrow.
6. agent-browser or Firecrawl only when route prediction says direct fetch is likely an app shell, blocked, rendered, or crawl-heavy page.
7. $opensrc when package implementation source is required.

Use codex-research plan "<query>" --profile quick|standard|deep|exhaustive to inspect call budgets before broad research. For replayable runs, initialize run state and pass --run to provider commands:

codex-research run init "<query>" --profile deep --topic github --out .codex/research/run.json
codex-research run status --run .codex/research/run.json

Native Codex web calls are not visible to the CLI. Debit them manually with codex-research run debit --run .codex/research/run.json --provider codex-web when they are part of the same budgeted run.

Firecrawl Policy

Firecrawl is a paid-capacity fallback lane, not the first source.

• Public docs: cache is allowed unless the task is latest-critical.
• Latest-critical pages: use --fresh so maxAge=0.
• Sensitive public pages: set --no-store-in-cache.
• Private/confidential/repo-proprietary content: do not send to Firecrawl unless the user explicitly allows external scraping for that material.
• If a page can be hydrated through GitHub, Context7, official docs, or direct fetch, prefer that before Firecrawl.

GitHub Policy

Use hybrid GitHub access:

• In Codex sessions, prefer the GitHub app/plugin for PRs, private repos, review threads, workflow logs, and authenticated repository metadata.
• Use codex-research github for standalone, replayable, and reportable REST calls. It falls back through GITHUB_TOKEN, GH_TOKEN, gh auth token, then public unauthenticated mode.
• Target and hydrate. Generate narrow query shards, respect search result and rate limits, then fetch full files, issue threads, releases, or compare ranges before citing.
• Escalate to clone/sparse checkout and local rg only when API search cannot prove the source-level claim.

Subagent Orchestration

When using subagents, follow $subspawn strict rendezvous behavior. The main Codex session spawns specialized research subagents, immediately waits for all spawned agents in the batch, then synthesizes. Research subagents must not spawn nested subagents.

Initial focused pack:

• deep_researcher: lead multi-source researcher and synthesis owner.
• github_researcher: GitHub repository/code/issues/releases specialist.
• context7_researcher: direct Context7 API docs specialist.
• openai_docs_researcher: official OpenAI docs specialist.
• source_validator: package/source/release implementation validator.
• citation_auditor: claim-to-source and freshness auditor.

Install templates with:

python3 skills/deep-researcher/scripts/install_agents.py --target project
python3 skills/deep-researcher/scripts/install_agents.py --target global

Evidence Bundles

For meaningful research, produce both machine and human outputs:

• JSONL ledger: .codex/research/ledger.jsonl
• source records JSON or cached source metadata
• route stats or cache stats when routing mattered
• Markdown report with concise claims and citations

Useful commands:

codex-research doctor
codex-research cache init
codex-research plan "research question" --profile deep
codex-research run init "research question" --profile deep --topic general --out .codex/research/run.json
codex-research fetch probe "https://example.com/docs"
codex-research context7 search --library "Next.js" --query "middleware auth"
codex-research github search-code 'repo:owner/repo symbol in:file'
codex-research ledger init
codex-research ledger add-source --from-cache <source-id>
codex-research report --ledger .codex/research/ledger.jsonl
codex-research eval

Stop Rules

Stop and mark UNVERIFIED when:

• sources disagree and you cannot identify the current authority;
• a required provider is rate-limited or missing credentials;
• only stale secondary sources are available;
• private material would need to be sent to an external provider without explicit permission;
• GitHub search is incomplete and hydration cannot validate the claim.