What is agent-papers-cli CLAUDE.md?

Project instructions for a repository containing command-line tools for reading academic papers and searching research sources. A command-line tool is a program operated from a terminal.

Developing, testing, or maintaining the paper-reading and paper-search tools, including their PDF parsing, search backends, caches, and saved research data.

It gives an agent the project’s structure, storage locations, entry points, and testing details so it can work consistently without guessing.

How collaborative-deep-research/agent-papers-cli configures Claude Cod

Reuse

Borrowing it

Nothing to install: this file belongs to collaborative-deep-research/agent-papers-cli. 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/collaborative-deep-research/agent-papers-cli/main/CLAUDE.md

Clone the repo

git clone --depth 1 https://github.com/collaborative-deep-research/agent-papers-cli

Made for: Claude Code.

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.

README.md

[![agentmods](https://agentmods.dev/badge/instructions/collaborative-deep-research/agent-papers-cli/claude-md/github.svg)](https://agentmods.dev/instructions/collaborative-deep-research/agent-papers-cli/claude-md)

Your own site

<a href="https://agentmods.dev/instructions/collaborative-deep-research/agent-papers-cli/claude-md"><img src="https://agentmods.dev/badge/instructions/collaborative-deep-research/agent-papers-cli/claude-md/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.

Your own site · 80×15

<a href="https://agentmods.dev/instructions/collaborative-deep-research/agent-papers-cli/claude-md"><img src="https://agentmods.dev/badge/instructions/collaborative-deep-research/agent-papers-cli/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 909 This file is loaded in full into every session.

When invoked 909 The same file — it is already loaded in full.

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.

Model	Per session	Once invoked
Fable 5.1	$0.00909	$0.00909
Opus 5.5	$0.00364	$0.00364
Sonnet 5.5	$0.00182	$0.00182
Haiku 4.5	$0.00091	$0.00091

Measured 2mo ago against content hash 240aa74c5dfc, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

agent-papers-cli 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 2mo 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.

CLAUDE.md · 39 lines

How it starts

The opening of the file, as written. The whole thing — 39 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Project: paper & paper-search CLI

Two CLI tools in one repo: paper (read academic PDFs) and paper-search (web + academic search). See README.md for full docs and SKILLS.md for agent workflows.

Quick reference

Entry points: paper = paper.cli:cli, paper-search = search.cli:cli (Click)
paper modules: cli.py, parser.py, fetcher.py, storage.py, renderer.py, models.py, highlighter.py, layout.py, bibtex.py
search modules: cli.py, config.py, models.py, renderer.py, backends/{google,semanticscholar,pubmed,browse}.py
Cache: ~/.papers/<paper_id>/ (papers: paper.pdf, parsed.json, metadata.json, highlights.json, layout.json, layout/*.png, paper_annotated.pdf, bibtex.bib), ~/.papers/.models/ (YOLO weights), ~/.papers/.env (persistent API keys), ~/.papers/.last_header (header auto-suppression state)
Local PDFs: Pass a file path (e.g., ./paper.pdf) instead of an arxiv ID — reads directly, no download. Cache uses {stem}-{hash8} IDs (SHA-256 of absolute path) to avoid collisions. Stale caches are detected via mtime comparison.
Tests: pytest — paper tests in tests/ (124 tests), search tests in tests/search/ (69 tests)
Agent skills: .claude/skills/ — research-coordinator, deep-research, literature-review, fact-check

Architecture notes

paper

Parser tries PDF built-in outline first, falls back to font-size heuristics
GROBID backend planned for future (noted in parser.py)
Data model inspired by papermage: flat raw_text + Section list with character-offset Spans
Downloads use atomic temp-file-then-rename pattern
Storage sanitizes paper IDs to prevent path traversal
Layout detection (optional [layout] extra) uses DocLayout-YOLO via doclayout_yolo
Layout detection is lazy: runs on first paper figures/tables/equations call, cached in layout.json
Supports MPS (Apple Metal), CUDA, and CPU backends for inference
Model weights auto-downloaded from collab-dr/DocLayout-YOLO-DocStructBench (pinned fork) to ~/.papers/.models/ on first use
Detected elements are cropped as PNG screenshots to ~/.papers/<id>/layout/

Read the full file on GitHub · 39 lines

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.

2mo ago First seen · 39 lines · 909 tokens per session scan A 240aa74c5dfc

Subscribe to this mod's changes

agent-papers-cli CLAUDE.md is an instructions file published in the GitHub repository collaborative-deep-research/agent-papers-cli (50 stars, last pushed 7mo ago), licensed Apache-2.0. It adds 909 tokens to every session, about $0.0036 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.

agent-papers-cli CLAUDE.md next to 6 instructions from other repositories
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agent-papers-cli: Instructions file for Claude Code