claude-code-my-workflow is a forkable setup for using Claude Code to produce and review academic papers, slides, data analyses, and replication packages. Researchers use its agents, skills, rules, hooks, and quality checks to coordinate these tasks and verify their results. The catalogue entries define the reusable workflow components for Claude Code.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add pedrohcgs/claude-code-my-workflow --skill diagnosegit clone --depth 1 https://github.com/pedrohcgs/claude-code-my-workflowWrote 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.
[](https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/diagnose)<a href="https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/diagnose"><img src="https://agentmods.dev/badge/skills/pedrohcgs/claude-code-my-workflow/diagnose.svg" alt="Measured on agentmods" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 3 findings, up to medium
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- medium Agent Snooping · line 215 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 216 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
- medium Agent Snooping · line 217 Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.
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.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00000 | $0.04097 |
| Opus 5 | $0.00000 | $0.02048 |
| Sonnet 5 | $0.00000 | $0.00819 |
| Haiku 4.5 | $0.00000 | $0.00410 |
Grade A, and why
diagnose 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 8d 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.
How it starts
The opening of the file, as written. The whole thing — 227 lines — stays where its author put it; the contents beside it link to each section on GitHub.
/diagnose — Root-Cause a Wrong or Failing Result
Find why an analysis errors, returns the wrong number, or won't reconcile — with a structured debugging loop rather than scattershot edits. Adapted from the diagnose pattern in mattpocock/skills, reshaped for empirical research code where the bug is usually a silent wrong number, not a crash.
The discipline: never edit before you can reproduce, and never fix before you can explain. A guessed fix that makes the symptom disappear without a named root cause is how a wrong number gets laundered into a published table.
When to use
- A regression / estimate returns a value you can't explain, or one that changed when nothing should have.
- A script errors out and the stack trace doesn't point at the real cause.
- A result "won't reproduce" — different number on re-run, on another machine, or after a package update.
- A replication claim fails
/audit-reproducibilityand you need to localize which step drifted.
Diagnose is symptom-driven and single-target: ONE wrong number / ONE failing run. Use a sibling instead when the job is different:
/audit-reproducibility— verify all numeric claims in a manuscript against current code (claim-driven, whole-paper). If you have one FAILing claim and want to localize which pipeline step produced it,/audit-reproducibilityhands off to/diagnose; if you want to re-check every table number, start there./review-r— code-quality review with no specific symptom./capture-environment— snapshot the environment when version/seed drift is the suspect.
Phases
Phase 0 — Pin the symptom (expected vs. actual)
State the bug as a falsifiable gap before touching anything:
- Expected: the value/behaviour you believe is correct, and why (a prior run, a paper table, a hand calculation, a theoretical sign).
- Actual: the value/error observed now, copied verbatim (full message, not a paraphrase).
- Tolerance: the threshold that separates "same" from "different", keyed to the source of expected — prior run on the same machine → machine-epsilon + display rounding; a published table → rounding + small slack (~1e-3); a hand calculation → ~0.01; a theoretical prediction → an economic-significance band, not a decimal. Don't chase 1e-12 floating-point noise; don't wave away a 5% gap. (See
replication-protocol.md.)
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.
- 8d ago First seen · 227 lines · 0 tokens per session scan A 42f48c2479fa
diagnose is a skill published in the GitHub repository pedrohcgs/claude-code-my-workflow (1,566 stars, last pushed 14d ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 4,097 tokens. 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.
Other skills, from other repositories
paper-workflow
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r-econometrics
Run IV, DiD, and RDD analyses in R with proper diagnostics.
issue-patrol
Automated GitHub issue scanning, triage, and fix loop.
econ-management-paper-polish
A writing and editing guide for papers in economics, management, finance, accounting, marketing, information systems, public administration, and related fields.
wrong-number-debugging
Use the moment a computed result looks wrong, surprising, suspicious, or "off" — a total that doesn't reconcile, revenue that tripled after a join, a mean that moved, a coefficient with the wrong sign, a count that's too high or too low, a metric that disagrees with another team's. Bisects the data pipeline to find…
stata-environment-diagnose
Diagnose local Stata, MCP, package, startup, graph-export, and permissions issues. Use when setup is failing, Stata is not discovered, packages are missing, logs are truncated, or a managed machine behaves differently from a normal workstation.