README

A set of fourteen agents for a research workflow that searches for papers, removes duplicates, plans reading, reads PDFs, extracts claims, and updates shared checkpoints. The agents pass work between stages.

In plain words
What is it for?
Use it to search academic papers, build and clean a research corpus, plan reading, extract information from PDFs, and track research outputs.
Why use it?
It provides a defined process for moving from a literature search to organized evidence. Shared checkpoints help each stage know what previous stages produced.

Agent for Claude Code

Install

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.

agentmods
npx agentmods add agents/angadhn/botference/readme
Clone the repo
git clone --depth 1 https://github.com/angadhn/botference

Made for: Claude Code.

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 1,234 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. Scan, not verified.
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 $0.00000 $0.01234
Opus 5 $0.00000 $0.00617
Sonnet 5 $0.00000 $0.00247
Haiku 4.5 $0.00000 $0.00123

Measured 2d ago against content hash aef691bdbef5, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

README 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 2d 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/README.md · 67 lines

How it starts

The opening of the file, as written. The whole thing — 67 lines — stays where its author put it; the contents beside it link to each section on GitHub.

[!NOTE] This README was AI-generated. I (Angadh) have not manually authored this nor checked it.

Agents — Planner's Menu

Fourteen agents forming the Botference loop. Each reads checkpoint.md, produces outputs, updates checkpoint, and yields. All agents inherit shared protocol from agent-base.md.

Custom workspace agents (in project .claude/agents/) override framework agents of the same name and declare their tools in a ## Tools section.

Agent Reference

Agent Role Tools (beyond essentials) Upstream → → Downstream Assign when…
scout Search + score papers pdf_metadata, citation_lookup/verify/verify_all, citation_manifest/download, validate_paper_ledger, render_paper_ledger_markdown, validate_support_requests user/planner triage Starting literature search or filling gaps
triage Dedup corpus, resolve grade conflicts, generate reading plan pdf_metadata, citation_verify_all, validate_paper_ledger, render_paper_ledger_markdown scout deep-reader After scout completes a round
deep-reader Read PDFs, extract claims/data, map sections pdf_metadata, extract_figure, validate_paper_ledger, render_paper_ledger_markdown, validate_support_requests triage critic, provocateur, synthesizer After triage produces a reading plan
critic Assess structure; check style/journal/figure compliance; propose figures check_language, check_journal, check_figure, check_claims, citation_verify_all deep-reader (survey), paper-writer (STYLE-CHECK), editor (compliance) provocateur, synthesizer (survey); paper-writer (STYLE-CHECK); research-coder (FIGURE-PROPOSAL) After deep-reader finishes, or after each paper-writer section
provocateur Stress-test: negative space, inverted assumptions, cross-domain bridges deep-reader + critic synthesizer After critic's survey assessment
synthesizer Merge findings into synthesis narrative + outline citation_lint, citation_verify_all deep-reader + critic + provocateur paper-writer After all analysis agents complete
paper-writer Write/revise sections; review editor changes check_language, citation_lint, validate_support_requests synthesizer (write), critic (revise), editor (REVIEW-EDITS) critic (STYLE-CHECK), editor When outline is ready or revisions approved
editor Substantiated edits to .tex with evidence backing check_claims, check_language, citation_lint, citation_verify_all paper-writer coherence-reviewer, paper-writer (REVIEW-EDITS) After paper-writer completes a section
coherence-reviewer Post-editing: promise-delivery, terminology, contradictions, novelty claims check_claims, check_language editor editor (fixes) After all sections are edited
research-coder Analysis scripts, simulations, figures from data critic (FIGURE-PROPOSAL), planner figure-stylist (figures), paper-writer (data) When figures proposed or data analysis needed
figure-stylist Visual clarity + print readiness review check_figure research-coder research-coder (revise) or next phase After each figure is generated
coder Read, modify, and test application code planner planner (task complete) When implementation tasks require source code changes
refactorer Restructure code to reduce duplication planner planner (task complete) When task says "refactor"
orchestrator AI-driven dispatch at phase boundaries read_file, list_files planner parallel/serial agents When Architecture is orchestrated

Read the full file on GitHub · 67 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. 2d ago First seen · 67 lines · 0 tokens per session scan A aef691bdbef5

Subscribe to this mod's changes

README is an agent published in the GitHub repository angadhn/botference (19 stars, last pushed 2d ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 1,234 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.

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