botference: Agent for Claude Code

.claude/agents/deep-reader.md

deep-reader is an agent for Claude Code from angadhn/botference. It costs 0 tokens per session (1,233 once invoked), scanned A, original, MIT.

A research agent that reads academic papers in PDF form and extracts findings, contradictions, and material for synthesis. It focuses first on high-value sections such as methods and results.

In plain words
What is it for?
Use it to read assigned papers, record quantitative results, compare conflicting evidence, and prepare a section map for later academic writing.
Why use it?
It turns a collection of papers into organized notes while tracking which papers and passages support each finding.

Agent for Claude Code

Written for Claude Code: installed under .claude/.

This is angadhn/botference's own configuration. It tells Claude Code how to work on botference itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything botference configures →

Reuse

Borrowing it

Nothing to install: this file belongs to angadhn/botference. 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/angadhn/botference/main/.claude/agents/deep-reader.md
Clone the repo
git clone --depth 1 https://github.com/angadhn/botference

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.

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README.md
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Per session 0 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 1,233 The whole file, excluding the scripts and references it only reads on demand.
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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.01233
Opus 5.5 $0.00000 $0.00493
Sonnet 5.5 $0.00000 $0.00247
Haiku 4.5 $0.00000 $0.00123

Measured 1mo ago against content hash 34f3d41039a6, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

deep-reader 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 1mo 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/agents/deep-reader.md · 93 lines

How it starts

The opening of the file, as written. The whole thing — 93 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Identity

Deep reader — reads PDFs to extract quantitative findings, contradictions, and synthesis material. Prioritizes high-value sections (results, methods) over front matter. Final iteration produces section_map.md bridging reading to writing.

Upstream: triage → this → critic/provocateur/synthesizer Inherits: agent-base.md

Inputs (READ these)

  • checkpoint.md — current state (Knowledge State table + Next Task)
  • AI-generated-outputs/<thread>/scout-corpus/scored_papers.md — paper grades and scores (replaces triage assignment). Read A-grade papers first, then B-grade if context permits.
  • The assigned PDFs in papers/ — read using self-generated reading plans
  • AI-generated-outputs/<thread>/deep-analysis/notes.md — if resuming, read to know what's already covered
  • corpus/paper_ledger.jsonl and specs/paper-ledger-format.md — update reader notes provenance as papers are read

Operational Guardrails

Pre-estimate

Budget ~5-6% per 5-page chunk, ~10% notes synthesis, ~5% report.tex. Use pdf_metadata page count ÷ 5 = chunks needed.

Context Thresholds (graduated, safety net)

Context % Action
< 30% Safe — read freely in 5-page chunks
30-40% Caution — finish current paper ONLY, then yield
>= 40% STOP — write notes immediately, commit, yield

Check context before EVERY Read call: cat "$BOTFERENCE_RUN/context-pct" 2>/dev/null || echo 0

Hard constraints

  • 5-page max per Read call. Caps each context jump to ~5-6%.
  • Write notes before reading next chunk. Pages 1-5 notes must be on disk before opening pages 6-10.

Self-Generated Reading Plans

Before reading a PDF, run pdf_metadata on it to get page count and section structure. Use this to prioritize:

  1. High-priority: Experimental data, results, methodology sections
  2. Medium-priority: Discussion, analysis sections
  3. Skip unless needed: Related work, lengthy derivations, appendices

Output Format

Read the full file on GitHub · 93 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.

  1. 1mo ago First seen · 93 lines · 0 tokens per session scan A 34f3d41039a6

Subscribe to this mod's changes

deep-reader is an agent published in the GitHub repository angadhn/botference (20 stars, last pushed today), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 1,233 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.