PhD-Zero: Skill for Codex

.agents/skills/deep-research/SKILL.md

deep-research is a skill for Codex from TenureAI/PhD-Zero. It costs 198 tokens per session (3,272 once invoked), scanned A, original, MIT.

A research process for finding, checking, and documenting evidence from multiple sources. It is intended for questions that need more than a quick answer, such as comparing options, investigating causes, or planning an approach.

In plain words
What is it for?
Use it for literature reviews, evidence-based comparisons, root-cause investigations, feasibility studies, design decisions, and implementation planning.
Why use it?
It helps replace unsupported conclusions with checked information and a clear record of where each finding came from.

Skill for Codex

Written for Codex: agents/openai.yaml present. Also seen: installed under .agents/ (shared by several agents); mentions Codex.

This is TenureAI/PhD-Zero's own configuration. It tells Codex how to work on PhD-Zero itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything PhD-Zero configures →

Reuse

Borrowing it

Nothing to install: this file belongs to TenureAI/PhD-Zero. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/TenureAI/PhD-Zero/main/.agents/skills/deep-research/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/TenureAI/PhD-Zero

Made for: Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for deep-research

README.md
[![agentmods](https://agentmods.dev/badge/skills/tenureai/phd-zero/deep-research/github.svg)](https://agentmods.dev/skills/tenureai/phd-zero/deep-research)
Your own site
<a href="https://agentmods.dev/skills/tenureai/phd-zero/deep-research"><img src="https://agentmods.dev/badge/skills/tenureai/phd-zero/deep-research/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for deep-research

Your own site · 80×15
<a href="https://agentmods.dev/skills/tenureai/phd-zero/deep-research"><img src="https://agentmods.dev/badge/skills/tenureai/phd-zero/deep-research.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 198 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,272 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00198 $0.03272
Opus 5.5 $0.00079 $0.01309
Sonnet 5.5 $0.00040 $0.00654
Haiku 4.5 $0.00020 $0.00327

Measured 1mo ago against content hash e206e03b6170, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

deep-research scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.agents/skills/deep-research/SKILL.md · 334 lines

How it starts

The opening of the file, as written. The whole thing — 334 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Deep Research

Mission

Produce a deeply researched, evidence-grounded answer with clear provenance and actionable conclusions, and act as the default gateway for external search in research runs.

Search Routing Gate (Mandatory)

All external search during non-trivial research runs must enter through deep-research.

Rules:

  1. do not bypass deep-research with ad hoc direct search when fresh outside evidence is needed
  2. deep-research may choose a lighter or deeper execution depth internally, but it may not silently skip actual search
  3. every deep-research run must perform real WebSearch calls and keep an auditable query trail
  4. if search is skipped because existing evidence is already fresh enough, emit dr_skip_reason with explicit date windows and source counts

Research Type Selection

Choose a primary research_type early:

  1. idea-exploration
  2. debug-investigation
  3. design-decision
  4. implementation-strategy
  5. conflict-resolution

If templates do not fit exactly, adapt structure freely but keep depth, verification, and citations.

Before selecting depth or running any WebSearch queries:

  1. confirm intake_checkpoint_complete=YES
  2. intake must at least define: objective/scope, constraints, and expected deliverable format
  3. route missing-information requests through human-checkpoint
  4. in moderate or detailed, prefer built-in user-question tool (request_user_input)
  5. if built-in tool is unavailable, degrade to concise plain-text questions
  6. if intake is incomplete, remain in clarification phase and do not run search, decomposition, or synthesis

Frontier-First Scout (Mandatory)

Every deep-research run must begin with a frontier-first scout before final depth selection.

Scout requirements:

  1. run at least 6-10 queries total
  2. cover at least:
    • bleeding-edge topic queries
    • frontier topic queries
    • one verification query family
    • one counter-evidence or criticism query family
  3. capture representative freshness, source quality, and contradiction density
  4. use scout evidence to choose final depth

Read the full file on GitHub · 334 lines

Files

What ships with it

4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 1mo ago First seen · 334 lines · 198 tokens per session scan A e206e03b6170

Subscribe to this mod's changes

deep-research is a skill published in the GitHub repository TenureAI/PhD-Zero (53 stars, last pushed 7mo ago), licensed MIT. It adds 198 tokens to every session and 3,272 once invoked, about $0.0008 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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