Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows
Agent Claude Code
Audits coherence between paper prose and replication outputs — catches hallucinated results, missing scripts, mismatched numbers, and unverifiable claims. Read-only with respect to project files; writes its own report at reviews/ /artifact-coherence-auditor/ .md. Complements code-paper-auditor (which maps numbers to…
Agent Claude Code
Peripheral vision audit for empirical output. Finds what the author cannot see — problems hiding in plain sight (vices) and opportunities being overlooked (virtues). Use when output exists and interpretation is about to happen. Inspired by Viktor Shklovsky's defamiliarization and a Jason Fletcher observation on Scott…
Agent Claude Code
Verify that cited claims in a paper accurately represent what the source papers actually say. Checks every factual claim against its reference. Read-only with respect to project files (paper, bib, cited PDFs); writes its own Claim Verify Report and typed citation-integrity component at reviews/ /claim-verify/ ..…
Agent Claude Code
Use this agent when you need to verify code-paper consistency — mapping every quantitative claim in a paper to its source code and output files. Launch in fresh context to avoid self-bias when auditing code written in a previous session. Produces a structured verification report with PASS/FAIL per claim. Examples…
Agent Claude Code
Multi-persona orchestrator for adversarial review of R, Python, Julia, or Stata research scripts. Runs an 11-category baseline checklist, then dispatches 3-6 specialist sub-agents (correctness, reproducibility, design, plus optional domain / performance / security) in parallel. Deduplicates findings across reviewers…
Agent Claude Code
Code review and research agent that delegates to OpenAI Codex CLI in headless mode. Use when you need an independent AI perspective on code, scripts, architecture, or technical questions. Examples: Example 1: user: "Ask Codex to review this script for bugs" assistant: "I'll launch the codex-research agent to get an…
Agent Claude Code
Research-focused substantive correctness agent. Checks mathematical derivations, assumption completeness, citation fidelity, code-theory alignment, and backward logic. Read-only with respect to project files (paper, bib, code, data); writes its own report at reviews/ /domain-reviewer/ .md. Examples: Example 1: user…
Agent Claude Code
Fast pre-review check for fatal errors in LaTeX papers. Launch BEFORE full review agents (paper-critic, domain-reviewer, referee2-reviewer). Binary PASS/FAIL verdict in 15-30 seconds. Checks compilation, placeholders, broken references, number contradictions, and section completeness. Examples: Example 1: user: "Quick…
Agent Claude Code
Generic fix implementer for any critic report. Reads CRITIC-REPORT.md, applies fixes by priority (Critical → Major → Minor), recompiles, and produces FIX-REPORT.md. Does not make independent editorial decisions — follows the critic's instructions precisely. Examples: Example 1: user: [main session launches fixer after…
Agent Claude Code
Web research agent that delegates to Gemini CLI in headless mode. Use when you need current web information, alternative AI perspectives, or broad search that complements the client's native web search. Examples: Example 1: user: "What are the latest developments in carbon auction design?" assistant: "I'll launch the…
Agent Claude Code
Adversarial auditor for LaTeX papers. Read-only with respect to project files (paper, bib, code, data); writes its own report at reviews/ /paper-critic/ .md plus a findings.json sidecar. Finds problems without fixing them — produces a structured report with scored issues that the fixer agent can action. Assumes the…
Agent Claude Code
Use this agent when you need to review someone else's paper — as a peer reviewer, discussant, or for reading group preparation. This agent reads the PDF carefully using split-pdf methodology, spawns parallel sub-agents for citation validation, novelty assessment, and methodology review, scans for hidden prompt…
Agent Claude Code
Use this agent when you need to review a research proposal, extended abstract, conference submission outline, or pre-paper plan — either his own or someone else's. Unlike the peer-reviewer (which reviews full papers), this agent is designed for incomplete work where the contribution is promised rather than delivered.…
Agent Claude Code
Rigorous adversarial reviewer for papers, manuscripts, research designs, code, and arguments. Supports standard, deep, grounded, and council review modes through client-neutral fresh-context and verification mechanisms. May write only its declared report and explicitly scoped replication artifacts.
Agent Claude Code
Reviews research workflows for reproducibility gaps — hidden dependencies, absolute paths, undocumented prerequisites, environment assumptions, and output traceability. Use when checking whether a project can be rerun by someone else or handed off cleanly. Read-only with respect to project files; writes its own report…