# Deep Research

> Perform auditable research with executable mode budgets, mandatory source-content verification, typed web and repository evidence, confidence assessment, honest degradation, and one fixed nine-section report. Use for web research, claim verification, technical comparisons, trend analysis, pure codebase research, and hybrid codebase-plus-web investigations that need traceable conclusions rather than search-result summaries.

- Skill: `johnqtcg/deep-research` (Agent Skill, multi-file: 45 files)
- Install (CLI): `npx skillmds@latest add johnqtcg/deep-research`
- Raw SKILL.md: https://api.skillmd.com/api/skills/johnqtcg/deep-research/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Docs & Writing
- Author: johnqtcg (https://skillmd.com/u/johnqtcg)
- Updated: 2026-09-21
- Page: https://skillmd.com/skills/johnqtcg/deep-research

---


# Deep Research

Produce research whose claims can be traced to content actually read or repository artifacts actually observed.

## Quick Reference

| Need | Action |
|---|---|
| Classify `web \| codebase \| hybrid` and `quick \| standard \| deep` | Run `plan` before retrieval |
| Enforce cumulative query, extraction, and report-source ceilings | Reuse the session artifact created by `plan --output` |
| Author findings JSON | Load `references/output-contract-template.md` |
| Assess hallucination, confidence, or source quality | Load `references/hallucination-and-verification.md` |
| Understand Web trust boundaries and safe egress | Load `references/web-evidence-and-egress.md` |
| Apply programmer-specific query/evidence patterns | Load `references/research-patterns.md` |
| Claim runtime behavior from tests | Load `references/test-receipt-schema.md` |

## Mandatory Gates

Execute gates in strict order. Stop when a gate blocks later work.

```
1) Scope → 2) Ambiguity → 3) Evidence → 4) Research Mode
    → 5) Hallucination Awareness → 6) Budget Control
    → 7) Content Extraction → 8) Execution Integrity
```

### 1) Scope Classification Gate

Select one research kind and one goal.

- Research kind: `web | codebase | hybrid`
- Category: comparison, trend, claim verification, technical deep-dive, codebase audit
- Goal: Know, Compare, Verify, Recommend, or Audit

Run the executable classifier:

```bash
python3 ${CLAUDE_SKILL_DIR}/scripts/deep_research.py plan \
  --request "<user request>" \
  --output /tmp/research_plan.json
```

**Every command below is written `python3 scripts/deep_research.py ...` for
brevity; run it as `python3 ${CLAUDE_SKILL_DIR}/scripts/deep_research.py ...`.**
For `codebase` and `hybrid` work the working directory is the user's
repository, not this skill, so a bare relative path will not resolve. Write
every `--output` outside the repository under study.

The output is a versioned session ledger, not a disposable plan. Reuse that
exact file for every budget-consuming command in the research run.

Use `codebase` when the answer depends only on local code, commits, or test results. Do not perform web retrieval merely to manufacture URLs. Use `hybrid` only when external evidence is part of the question.

### 2) Ambiguity Resolution Gate

**STOP and ASK** when scope, comparison dimensions, time window, or success criteria would materially change the research. Do not ask again for constraints already supplied.

### 3) Evidence Requirements Gate

Define the evidence chain before retrieval.

| Conclusion Type | Minimum Evidence Chain | Target Confidence |
|---|---|---|
| Narrow single fact | 1 validator-controlled live capture + T1 re-derived from its effective final URL + exact supporting excerpt | High |
| Direct code fact | Code line/excerpt verified by reading the declared Git blob at an existing hexadecimal commit | High |
| Runtime code behavior | Every cited code item is pinned to one commit/tree + one host test receipt covers the finding and every code ID, names every tested path, passes relevance review, and matches that clean snapshot | High |
| Best-practice recommendation | 1 primary basis + 2 independent practitioner or empirical sources | Medium–High |
| Technology comparison | 3 independent benchmarks/reviews with methodology | Medium |
| Trend/adoption claim | 2 data sources from different periods | Medium |
| Disputed or fast-moving topic | 4 sources across tiers + explicit conflict treatment | Tiered |

Each finding must also carry a claim-support review. Excerpt containment
proves the quotation is real; it does not prove the quotation supports the
sentence built on it. These are two verdicts and the report prints both.

```json
"support_review": {
  "stance": "supports",
  "rationale": "why this excerpt entails this claim",
  "reviewed_by": "author"
}
```

`stance` is one of `supports | partial | context-only | contradicts`. A missing
block is `unreviewed`, never an implicit pass, and caps the finding below High.
A polarity or unquoted-number screen can only remove support, never grant it;
a screened conflict without an attestation makes the finding unusable.

Use typed evidence:

- Web: `{"kind":"web","url":"...","excerpt":"exact text from content.json"}`
- Code: `{"kind":"code","id":"code-1"}`
- Commit: `{"kind":"commit","id":"commit-head"}`
- Test: `{"kind":"test","id":"test-1"}`

Bare `citations` URLs are legacy inputs. Treat them as unverified because they do not prove extraction or claim support.

### 4) Research Mode Gate

Auto-select mode with `plan`; pass an explicit user mode as `--mode`.

| Signal | → Mode |
|---|---|
| Single factual question, "quick check" | Quick |
| Default research task | Standard |
| Thorough/deep request, multi-vendor decision, architecture/trend report | Deep |
| Security-sensitive or production-impacting decision | Deep |

| Mode | Retrieval ceiling | Extraction ceiling | Report-source ceiling | Typical range (advisory) |
|---|---:|---:|---:|---|
| Quick | 10 | 5 | 8 | 5–10 retrievals, 3–8 sources |
| Standard | 25 | 10 | 20 | 15–25 retrievals, 8–20 sources |
| Deep | 50 | 15 | 40 | 30–50 retrievals, 15–40 sources |

Only the three ceilings are executable. The advisory column is guidance for
planning a run; no command enforces a floor, so a Quick report citing two
sources is not rejected.

If the user explicitly requests a mode, use it. Classification is deterministic and behavior-tested.

### 5) Hallucination Awareness Gate

Never fabricate citations, URLs, source metadata, code locations, commits, or test results.

| Risk Level | Information | Verification Method |
|---|---|---|
| High | API signature/configuration | Official primary documentation + validator-controlled live capture + extracted excerpt |
| High | Benchmark/statistic | Original data and disclosed methodology |
| High | Security/compliance | Official advisory, standard, or regulator |
| High | Repository behavior | Code evidence and, for runtime behavior, a passing test |
| Medium | Architecture recommendation | Independent sources with limitations |

Read `references/hallucination-and-verification.md` for confidence and source-quality rules.

### 6) Budget Control Gate

Use the selected mode as an executable ceiling:

```bash
python3 scripts/deep_research.py retrieve \
  --session /tmp/research_plan.json \
  --query "<subtopic 1>" \
  --query "<subtopic 2>" \
  --output /tmp/results.json
```

The parser rejects more than 10, 25, or 50 queries in one Quick, Standard, or
Deep invocation, and the ledger enforces the same ceilings across repeated
invocations, so two calls cannot each consume the full allowance. The hard
ceiling is 50 retrieval calls per Deep session; one query is one call.

`fetch-content` defaults to the remaining session extraction allowance and
rejects an explicitly larger per-invocation `--limit`.
When more candidate URLs exist than the ceiling permits, it records `budget_exhausted=true`; bundled `validate` and `report` commands consume that state automatically.

Before bypassing `retrieve` or `fetch-content` with a host `WebSearch` or
`WebFetch` tool, reserve the equivalent count in the same ledger:

```bash
python3 scripts/deep_research.py reserve-budget \
  --session /tmp/research_plan.json \
  --budget retrieval_calls \
  --count 1 \
  --output /tmp/budget_reservation.json
```

Final live re-verification has its own budget line, `live_verifications`
(Quick 5 / Standard 10 / Deep 15), because it opens real sockets. `validate`
and `report` therefore require `--session` whenever `--live-web` is passed.
When cited pages outnumber the remaining allowance the command verifies as many
as the ledger permits, marks budget exhaustion, and degrades to Partial rather
than fetching past the ceiling.

The ledger is an operational concurrency-safe constraint, not a tamper-proof
audit log. It cannot account for tool calls that bypass both the bundled
commands and `reserve-budget`. `plan` refuses to overwrite an existing ledger.
Locking uses `fcntl` on POSIX and `msvcrt` byte locking on Windows, failing
closed if neither exists. The regression suite performs a real multi-process
contention test on fork-capable POSIX; the Windows backend still requires
Windows CI coverage.

### 7) Content Extraction Gate

For `web` and `hybrid`, fetch actual content before synthesis:

```bash
python3 scripts/deep_research.py fetch-content \
  --session /tmp/research_plan.json \
  --results /tmp/results.json \
  --output /tmp/content.json
```

Each web evidence object must identify an exact excerpt found in a successfully extracted item. A search snippet, reachable URL, or failed/low-yield page cannot support a finding.

Content extraction is mandatory for web and hybrid research.

`fetch-content` accepts only public `http`/`https` targets, connects to an
already validated IP while preserving hostname verification, and revalidates
before every redirect hop. See `references/web-evidence-and-egress.md`.

Live verification reads the whole page: it lifts both the authoring download cap
(512 KB) and the extraction cap (15,000 characters), because a correct excerpt
from the tail of a long reference page could otherwise never match. Excerpt
matching also folds typographic variants — curly quotes, dashes, non-breaking
spaces, backticks — so a page's rendering cannot reject a quote that is right.

Treat a saved `content.json` as an untrusted authoring artifact. Loading it
always clears `live_verified`, so it may support Medium after excerpt matching
but never primary status or High. Web High requires `--live-web` on the final
`validate` or `report`, which refetches each cited URL through the safe
transport and derives tier/type from the effective final URL. Caller-provided
authority fields never grant authority.

For `codebase`, use `search-codebase`; content extraction is not required:

```bash
python3 scripts/deep_research.py search-codebase \
  --pattern "verifyToken" \
  --root /path/to/repo \
  --output /tmp/code_evidence.json
```

`search-codebase` pins clean tracked content to the real HEAD object ID and
emits modified, staged, or untracked content as `working-tree-unpinned`, which
cannot support a High direct-code finding. The validator rereads
`<commit>:<path>` and compares the declared line, excerpt, and commit subject.

Execute a focused test once through the host's normal permission path. Then
create a `deep-research/host-test-receipt-v2` receipt and import it:

```bash
python3 scripts/deep_research.py snapshot-codebase \
  --root /path/to/repo \
  --output /tmp/repository_snapshot_before.json

go test -run TestVerifyToken ./auth

python3 scripts/deep_research.py snapshot-codebase \
  --root /path/to/repo \
  --output /tmp/repository_snapshot_after.json

python3 scripts/deep_research.py import-test-receipt \
  --receipt /tmp/host_test_receipt.json \
  --code-evidence /tmp/code_evidence.json \
  --output /tmp/code_and_test_evidence.json
```

`snapshot-codebase` only reads repository root, HEAD, tree hash, and dirty
state; write its output outside the repository. The host compares before/after
snapshots and copies the unchanged clean identity into the receipt. The helper
never executes receipt argv.

Runtime High treats the finding's complete code evidence set as atomic: one
receipt must cover the finding, every code ID, and every tested path on one
clean commit/tree. This skill pre-approves only Go, pytest, and unittest
commands. Load `references/test-receipt-schema.md` for the full contract,
including receipt-coverage failure modes and other frameworks.

### 8) Execution Integrity Gate

- Do not present hypothetical findings if retrieval or repository inspection did not run.
- Distinguish "source says X" from "snippet mentions X".
- Report the actual number of retrieved, successfully extracted, repository, and cited evidence units.
- Run `validate` before manual synthesis checks.
- Always let `report` auto-run the same validation path.
- For a final Web report, perform live verification once with
  `report --live-web --validation-output ...`; do not first run
  `validate --live-web` unless a second fresh network check is intentional.
- Omit unsupported findings from substantive report sections and expose the reason in Gaps.

## Unified Workflow

For a Quick single-fact check, collapse the collection half into one command:

```bash
python3 scripts/deep_research.py quick-check \
  --request "<narrow question>" \
  --claim "<the claim to verify>" \
  --workdir /tmp/qc
```

It plans, retrieves, extracts, and writes a findings skeleton with the
candidate evidence already in place. Fill in each excerpt and `support_review`,
save as `findings.json`, then run the single `report --live-web` it prints.
Every gate still applies. For Standard and Deep work, use the numbered steps
below.

1. Run `plan`; record kind, mode, and budgets. When it reports a
   classification confidence below `high`, confirm the routing or rerun with
   `--research-kind` / `--mode`; a deterministic keyword rule always answers,
   which is not the same as answering correctly.
2. Split the question into 2–4 subtopics.
3. Collect required artifacts:
   - `web`: `retrieve` → `fetch-content`
   - `codebase`: `search-codebase`; for runtime claims, snapshot the repository, execute one focused host test, snapshot again, and `import-test-receipt`
   - `hybrid`: both paths
4. Author `findings.json` with typed evidence and exact excerpts.
5. Optionally run offline `validate` with every required artifact to catch
   shape/excerpt errors. Offline serialized Web evidence is capped below High.
6. Run `report`; for final Web/Hybrid High eligibility, pass `--live-web`.
   It performs the fresh verification once, writes `--validation-output`,
   derives the executive summary from usable findings, and renders the
   canonical contract.
7. Deliver the report without renaming, splitting, or omitting top-level sections.

Run `validate` with the same evidence flags when validation itself is the
deliverable; `--live-web` and `--check-live` both open real sockets, so both
require `--session` and both draw on `live_verifications`. `validate` and
`report` also refuse artifacts stamped with a different `session_id` than the
ledger you pass, so the budget line in the report always describes the run that
produced the evidence. When a report is
required, prefer a single `report --live-web` so the same pages are not
fetched twice.

Final Web report:

```bash
python3 scripts/deep_research.py report \
  --question "<question>" \
  --research-kind web \
  --results /tmp/results.json \
  --content /tmp/content.json \
  --findings /tmp/findings.json \
  --session /tmp/research_plan.json \
  --live-web \
  --validation-output /tmp/validation.json \
  --output /tmp/report.md
```

Pure codebase report:

```bash
python3 scripts/deep_research.py report \
  --question "<question>" \
  --research-kind codebase \
  --code-evidence /tmp/code_evidence.json \
  --findings /tmp/findings.json \
  --session /tmp/research_plan.json \
  --validation-output /tmp/validation.json \
  --output /tmp/report.md
```

## Confidence Rule

Use one rule everywhere:

- Require an attested claim-support review (`stance: supports`, no screened
  conflict, no unquoted number) for every `High`. Citation integrity and claim
  support are separate gates and High needs both.
- Allow `High` for a narrow single fact only when the current validator/report
  process freshly fetched the cited page, matched the excerpt, and re-derived
  T1 from the effective final URL.
- Allow `High` for a direct code fact only after the validator rereads and matches pinned Git content.
- Allow `High` for runtime behavior only when every cited code item is pinned to one Git commit/tree and one reviewed host receipt covers the finding, all code IDs, and all tested paths on that same clean snapshot.
- Require two independent verified units, including a primary unit, for all other `High` findings.
- Downgrade to `Medium` when some verified support exists but the High rule is unmet.
- Use `Low` only for deliberately tentative claims that still have verified support.
- Mark unusable and omit when no evidence validates.

The CLI records requested and effective confidence plus downgrade reasons.
Unpinned working-tree evidence may remain useful at Medium or Low when its
current file content validates, but it is never represented as belonging to
HEAD.

## Honest Degradation

| Level | Executable Condition | Action |
|---|---|---|
| **Full** | Required artifacts exist; every included finding meets requested confidence; no extraction failure | Deliver all nine sections |
| **Partial** | Usable findings remain, but a finding is downgraded, extraction partially fails, or the budget ends with non-critical gaps | Deliver all nine sections and name gaps |
| **Blocked** | A required artifact is missing, no finding has usable evidence, or budget exhaustion prevents the core chain | Stop claiming conclusions; emit or report only the blocked state and next evidence needed |

Bundled content artifacts propagate budget exhaustion automatically. Pass `--budget-exhausted` to `validate` or `report` when an external or manually assembled artifact reached its ceiling.

## Canonical Output Contract

Every Quick, Standard, and Deep report must use these exact 9 sections and top-level headings in this order:

1. `Research Question`
2. `Method`
3. `Executive Summary`
4. `Key Findings`
5. `Detailed Analysis`
6. `Consensus vs Debate`
7. `Source Quality Notes`
8. `Sources`
9. `Gaps & Limitations`

Quick mode may keep Detailed Analysis and Consensus vs Debate concise; it must not omit them. Load `references/output-contract-template.md` before authoring findings or delivering a report.

## Source Quality

Treat automated classification as conservative preclassification:

- Do not classify arbitrary `docs.*` hosts as official.
- Classify `.edu` as institutional, not automatically official product documentation.
- Emit T1–T5, classification basis, date or `unknown`, sponsorship, and methodology for each web source.
- Ignore caller-provided authority labels during validation. Re-derive
  tier/type from the normalized URL and, for live evidence, the effective final
  URL.
- Automatic T1 comes from two places only: recognized government namespaces,
  and `references/source-authority-registry.json`, a curated list binding a
  domain to a standards body, government or owning project with a stated basis
  and check date. Registry classifications carry a `registry:` basis so a
  checked ownership record is never confused with a URL-shape guess. An
  unlisted host keeps its heuristic tier; absence is not evidence of
  untrustworthiness.
- A project's own documentation is T1 about that project's own behavior and is
  simultaneously `vendor_self`. It cannot be the independent primary unit for a
  comparison, benchmark or recommendation.
- Surface unknown sponsorship/methodology rather than guessing.

Use the default tiers in `references/hallucination-and-verification.md`.

## Safety Rules

1. Never fabricate evidence or execution state.
2. Require typed support for every substantive claim.
3. Ensure contradictory evidence is surfaced under Consensus vs Debate.
4. Do not convert repository artifacts into fake web citations.
5. Stop or degrade when required evidence is missing.
6. Route every bundled Web request through the public-network-only transport;
   never add a raw `urlopen` bypass.
7. Never let serialized Web metadata or content assert that live verification
   occurred.

## Anti-Examples — DO NOT Do These

1. **Synthesize from snippets** — extract the page and cite an exact supporting excerpt.
2. **Attach a URL without support text** — a URL proves location, not claim support.
3. **Quote page source instead of rendered text** — an excerpt copied from
   markup (`tr><th>Default:</th><td>all</td></tr`) or assembled into a list you
   wrote yourself is not a quotation and will not validate.
4. **Treat a matched excerpt as a supported claim** — containment proves the
   quote is real, not that it backs the sentence. Review the claim against the
   excerpt and record the stance; a claim that inverts its own quote is unusable.
5. **Call one generic source "official" because its host starts with docs** — the registry binds a domain to an owner; a URL shape does not.
6. **Call every High finding a two-domain claim** — apply the narrow T1 single-fact exception.
7. **Call every one-source claim High** — the exception requires T1 primary content and a narrow fact.
8. **Force repository facts into fake web citations** — cite code, commit, and test evidence IDs.
9. **Treat exit code 0 or partial receipt coverage as semantic proof** — require a focused selector and one receipt covering the finding plus the complete same-snapshot code set.
10. **Generate a report without content for web research** — the parser must stop.
11. **Split Consensus and Debate into top-level headings** — keep both under section 6.
12. **Exceed a mode budget** — stop, mark budget exhaustion, and degrade honestly.
13. **Trust caller-authored T1 or `live_verified` fields** — re-fetch in the
    validator and re-derive authority from the effective final URL.
14. **Fetch `file:`, FTP, localhost, private, link-local, or metadata targets**
    — reject before reserving budget or opening a connection, including after redirects.

```
BAD: Finding (High): X is faster. citations=["https://example.com"]
GOOD: Finding (Medium): X was faster in this benchmark, with method limits. evidence=[{"kind":"web","url":"...","excerpt":"..."}]
```

## Load References Selectively

| When | → Load |
|---|---|
| Every report | `references/output-contract-template.md` — nine-section structure, findings schema, evidence and `support_review` examples |
| Quantitative, high-stakes, disputed, sponsored, or model-generated claims | `references/hallucination-and-verification.md` — verification, confidence, claim support, T1–T5, degradation |
| Debugging, APIs, code search, comparisons, benchmarks, standards, security | `references/research-patterns.md` — topic-specific query and evidence patterns |
| Any runtime-behavior finding backed by a test | `references/test-receipt-schema.md` — execute through the host once, then import and statically validate |

## Subcommands Reference

| Subcommand | Purpose | Key Flags |
|---|---|---|
| `plan` | Classify kind/mode and initialize a session ledger | `--request`, `--mode`, `--research-kind`, `--output` |
| `reserve-budget` | Reserve ledger usage before external host search/fetch | `--session`, `--budget`, `--count`, `--output` |
| `retrieve` | Search DDG Lite under cumulative budget | `--query`, `--session`, `--limit-per-query`, `--output` |
| `fetch-content` | Safely extract public HTTP(S) content under cumulative budget | `--results` or `--url`, `--session`, `--limit`, `--output` |
| `quick-check` | One-shot Quick collection plus a findings skeleton | `--request`, `--claim`, `--url`, `--workdir` |
| `search-codebase` | Produce per-file pinned or unpinned repository evidence | `--pattern`, `--root`, `--glob`, `--output` |
| `snapshot-codebase` | Read repository root, HEAD, tree, and dirty state without executing tests | `--root`, `--output` |
| `import-test-receipt` | Statically verify and append one host-created receipt | `--receipt`, `--code-evidence`, `--output` |
| `validate` | Re-read typed evidence and optionally live-verify cited Web pages | `--research-kind`, `--results`, `--content`, `--code-evidence`, `--findings`, `--session`, `--live-web`, `--timeout`, `--output` |
| `report` | Auto-validate, optionally live-verify Web evidence, enforce source ceiling, and render nine sections | `--question`, `--research-kind`, `--session`, evidence flags, `--live-web`, `--timeout`, `--validation-output`, `--output` |

## Search and Extraction Fallbacks

If DDG Lite fails, use an available search tool with the same query plan and preserve its result metadata. If static extraction fails, use a browser-capable fetcher and save equivalent content records. Imported records stay untrusted and cannot produce Web High; the bundled validator must still make its own safe live capture. Report the actual method used.

## Bundled Assets

The shipped file inventory lives in `references/bundled-assets.md`, where a
regression test compares it against the directory in both directions. A
hand-maintained list in this file had drifted by five files, including the
regression entry point and the suite that guards this document's own claims.