paper-trail-doctor

paper-trail-doctor is a command for Claude Code from roomi-fields/paper-trail. It costs 45 tokens per session (563 once invoked), scanned A, original, MIT.

A command for auditing a registry of research-paper references against 19 consistency rules.

In plain words
What is it for?
Use it to check the registry, generate a machine-readable report, recalculate PDF checksums, or apply supported automatic repairs.
Why use it?
It identifies errors, warnings, and information issues such as bad PDF paths, missing checksums, or incorrectly numbered download attempts, with safe fixes available for some problems.

Command for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the paper-trail plugin — 6 skills, 22 commands, 6 agents, 3 hooks shipped together

Good fit Use it to check the registry, generate a machine-readable report, recalculate PDF checksums, or apply supported automatic repairs.

Compare 6 commands from other repositories ↓
Install with agentmods
npx agentmods add commands/roomi-fields/paper-trail/paper-trail-doctor
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.

Clone the repo
git clone --depth 1 https://github.com/roomi-fields/paper-trail

Made for: Claude Code.

Or install paper-trail, the plugin that ships this one along with the rest of its 6 skills, 22 commands, 6 agents, 3 hooks.

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.

agentmods badge for paper-trail-doctor

README.md
[![agentmods](https://agentmods.dev/badge/commands/roomi-fields/paper-trail/paper-trail-doctor/github.svg)](https://agentmods.dev/commands/roomi-fields/paper-trail/paper-trail-doctor)
Your own site
<a href="https://agentmods.dev/commands/roomi-fields/paper-trail/paper-trail-doctor"><img src="https://agentmods.dev/badge/commands/roomi-fields/paper-trail/paper-trail-doctor/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.

agentmods 80×15 button for paper-trail-doctor

Your own site · 80×15
<a href="https://agentmods.dev/commands/roomi-fields/paper-trail/paper-trail-doctor"><img src="https://agentmods.dev/badge/commands/roomi-fields/paper-trail/paper-trail-doctor.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 45 Only the description is in the session, so the agent can decide to use it. The body loads when it is invoked.
When invoked 563 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 $0.00045 $0.00563
Opus 5 $0.00023 $0.00282
Sonnet 5 $0.00009 $0.00113
Haiku 4.5 $0.00005 $0.00056

Measured 10d ago against content hash 04da4a7ba280, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

paper-trail-doctor 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 10d 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.

commands/paper-trail-doctor.md · 63 lines

What it actually says

/paper-trail:doctor — Run invariants audit

Invoke the registry-doctor skill to check the 19 invariants on the registry.

Usage

/paper-trail:doctor                              # full check, severity ≥ info
/paper-trail:doctor --severity error             # errors only
/paper-trail:doctor --severity warn              # errors + warnings
/paper-trail:doctor --fix                        # apply safe auto-fixes
/paper-trail:doctor --fix --severity warn        # idem
/paper-trail:doctor --json                       # machine-readable output
/paper-trail:doctor --correlate-rtfm             # Couche 5 — RTFM crosscheck
/paper-trail:doctor --check-sha                  # slow — recompute all sha256

What it does

Delegates to the worker B :

python -m pipeline doctor [flags]

Returns a markdown (or JSON) report classifying violations by invariant and severity. Safe auto-fixes :

  • I4 : strip prefix 10_SOURCES/ from pdf_path if present
  • I6 : recompute pdf_sha256 from disk file if missing or malformed
  • I9 : renumber acquisition_attempts[].n to be strictly 1..N
  • I5 semi : if PDF missing on disk, transition to needs_reacquisition
  • I7 semi : if page1_validation_log inconsistent, transition to needs_reacquisition

Never auto-fixes (require human decision) :

  • I10 : empty blocked_reason — humain must categorize the blockage
  • I8 : non-monotonic state_history — likely a bug or migration artifact
  • I14 : transition out of terminal state — likely a manual mutation needing audit

Exit code

  • 0 : no errors (warns/infos may be present)
  • 1 : at least one ERROR remaining (after auto-fixes if --fix)

Useful for CI / pre-commit hooks.

Cross-reference

See also :

  • /paper-trail:status — overall registry state counts
  • /paper-trail:cascade — push refs forward (which doctor will audit)
  • pipeline/USAGE.md for the underlying worker B CLI
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. 10d ago First seen · 63 lines · 45 tokens per session scan A 04da4a7ba280

Subscribe to this mod's changes

paper-trail-doctor is a command published in the GitHub repository roomi-fields/paper-trail (5 stars, last pushed 7d ago), licensed MIT. It adds 45 tokens to every session and 563 once invoked, about $0.0002 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 2026-08-31.