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 permission-checkgit 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/permission-check)<a href="https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/permission-check"><img src="https://agentmods.dev/badge/skills/pedrohcgs/claude-code-my-workflow/permission-check/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.
<a href="https://agentmods.dev/skills/pedrohcgs/claude-code-my-workflow/permission-check"><img src="https://agentmods.dev/badge/skills/pedrohcgs/claude-code-my-workflow/permission-check.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector warn
SkillSpector: 8 findings, up to high
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 →
- high Agent Snooping · line 19 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 28 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 60 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 20 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 43 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 76 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 21 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
- high Agent Snooping · line 44 Skill reads from agent configuration directories (.claude/, .codex/, .gemini/). These directories may contain API keys, personal settings, and other credentials that the skill has no legitimate need to access.Fix: Remove all code or instructions that access agent configuration directories (.claude/, .codex/, .gemini/). If configuration values are needed, pass them explicitly as parameters or environment variabl
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 | $0.00111 | $0.01879 |
| Opus 5 | $0.00056 | $0.00940 |
| Sonnet 5 | $0.00022 | $0.00376 |
| Haiku 4.5 | $0.00011 | $0.00188 |
Grade B, and why
permission-check scanned grade B with 1 finding 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 9d 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.
Reads agent configuration directoriesmediumAgent snooping
.claude/, .codex/, .gemini/ hold keys, settings and other credentials a mod has no legitimate need for.
3. **CLI user settings** — `~/.claude/settings.json`. Key: `permissions.defaultMode`. How it starts
The opening of the file, as written. The whole thing — 147 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Permission Check
Purpose
Surface the full permission-mode picture across every layer Claude Code honors, so the user can see at a glance why prompts are (or aren't) firing. Claude Code resolves permission mode from a 6-tier stack; a single misconfigured layer produces silent overrides that are hard to debug by eye.
The 6 layers (precedence: bottom wins)
- VSCode user settings —
~/Library/Application Support/Code/User/settings.json(macOS),%APPDATA%/Code/User/settings.json(Windows),~/.config/Code/User/settings.json(Linux). Key:claudeCode.initialPermissionMode. - VSCode workspace settings —
<repo>/.vscode/settings.json. Same key. Wins over user. - CLI user settings —
~/.claude/settings.json. Key:permissions.defaultMode. - CLI project settings —
<repo>/.claude/settings.json. Same key. Wins over user. - CLI project-local settings —
<repo>/.claude/settings.local.json. Same key. Wins over project. - In-session mode — set at session start from layers 1-5, then mutable via
Shift+Tabor/permission-mode. Authoritative until session ends.
Key insight: initialPermissionMode only fires at session start. If you toggled mid-session (or the session started before a settings change), the file-level settings are correct but the runtime mode differs. That's the #1 source of "bypass isn't working" confusion.
Privacy contract
Host-global settings files (~/.claude/settings.json, VSCode user settings) may contain:
- Paths to unrelated projects and secrets
- API keys, tokens, or provider credentials added outside this repo
- Permission policies set by the user's org or employer
This skill is designed for defense-in-depth: Phase A runs automatically and reads only repo-local files. Phase B reads host-global files only after the user explicitly confirms — never silently. When reporting host-global layers, redact any key that is not directly relevant to permissions.* or claudeCode.*.
Protocol
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.
- 9d ago First seen · 147 lines · 111 tokens per session scan B 25f41a362d6b
permission-check is a skill published in the GitHub repository pedrohcgs/claude-code-my-workflow (1,569 stars, last pushed 15d ago), licensed MIT. It adds 111 tokens to every session and 1,879 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it B with 1 finding (reads agent configuration directories). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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