Borrowing it
Nothing to install: this file belongs to heleninsights-dot/phd-deepread-workflow. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/heleninsights-dot/phd-deepread-workflow/main/CLAUDE.mdgit clone --depth 1 https://github.com/heleninsights-dot/phd-deepread-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/instructions/heleninsights-dot/phd-deepread-workflow/claude-md)<a href="https://agentmods.dev/instructions/heleninsights-dot/phd-deepread-workflow/claude-md"><img src="https://agentmods.dev/badge/instructions/heleninsights-dot/phd-deepread-workflow/claude-md.svg" alt="Measured on agentmods" height="20"></a>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 | $0.01639 | $0.01639 |
| Opus 5 | $0.00820 | $0.00820 |
| Sonnet 5 | $0.00328 | $0.00328 |
| Haiku 4.5 | $0.00164 | $0.00164 |
Grade A, and why
phd-deepread-workflow CLAUDE.md 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 — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
Commands
# Install
pip install -r requirements.txt # core deps (PyMuPDF, pytesseract, Pillow)
pip install -r requirements-dev.txt # dev deps (pytest, black, flake8, mypy)
brew install tesseract # required OCR engine (macOS)
# Test
make test # run all tests
pytest tests/test_canvas.py -v # run single test file
pytest -m "not slow" # skip slow tests (markers: slow, integration)
make test-cov # with coverage report
# Code quality
make lint # flake8
make format # black + isort
make type-check # mypy
make check # all of the above + test
# Build & publish
make build # creates dist/
make publish-test # upload to TestPyPI
make publish # upload to PyPI
# Run the CLI locally
phd-deepread doctor # check dependencies
phd-deepread extract paper.pdf -o markdown_output/
phd-deepread generate markdown_output/paper/
phd-deepread reformat markdown_output/paper/ # prompt to clean extraction → <paper>_formatted.md
phd-deepread canvas --title "Title" --authors "Author" --year "2024"
phd-deepread run paper.pdf # full pipeline: extract → generate → canvas
phd-deepread batch papers/ -o output/
phd-deepread verify markdown_output/paper/
Architecture
The CLI entry point is scripts/phd_deepread.py:main(), which dispatches commands to individual scripts via subprocess. Commands map to:
| Command | Script | Role |
|---|---|---|
doctor (alias setup) |
scripts/doctor.py |
Dependency / first-run check |
extract |
scripts/extract.py |
PDF → Markdown + images |
generate |
scripts/generate.py |
Markdown → Claude prompt (structured literature note) |
reformat |
scripts/reformat.py |
Extracted Markdown → Claude prompt that cleans it into an Obsidian-ready layout |
canvas |
scripts/canvas.py |
→ 9-node JSON Canvas file (optionally populated from a finished note via --from-note) |
run |
scripts/process.py |
Orchestrates extract → generate prompt → canvas → reformat prompt |
verify |
scripts/verify.py |
Quality checks on output directory |
batch |
scripts/batch.py |
Loop run over a folder of PDFs |
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 · 96 lines · 1,639 tokens per session scan A d00ccfd391c8
phd-deepread-workflow CLAUDE.md is an instructions file published in the GitHub repository heleninsights-dot/phd-deepread-workflow (61 stars, last pushed 2mo ago), licensed MIT. It adds 1,639 tokens to every session, about $0.0082 per session on Opus 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.
Other instructions, from other repositories
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
spec-kit AGENTS.md
AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.