paper-trail

Plugin paper-trail in roomi-fields/paper-trail. Commands read from the repo's manifest — 1 month ago.

Skills (6)

• citation-receipts

  Systematic per-citation verification protocol for academic writing. MUST be used whenever writing content that cites sources — papers, blog posts, SOTAs, or any document making factual claims about external work. Triggers (FR + EN) on any writing task involving references, citations, or bibliographi

• paper-writer

  Write academic papers (IMRaD structure) for conferences and journals, with mandatory anti-hallucination citation verification. Triggers (FR + EN) : "écris un paper", "article pour conférence", "rédige pour la conférence", "structure IMRaD", "soumission paper", "write a paper on", "academic article",

• pdf-cascade

  Acquire PDFs for bibliographic references via a strict 8-source cascade (Crossref OA → arXiv → OpenAlex → Unpaywall → HAL → CORE → archive.org → WebSearch queue; optionally Sci-Hub + Anna's Archive, plus Anna's via a windowed browser, in opt-in mode). Each acquired PDF is validated against expected

• registry-doctor

  Audit the bibliography registry for consistency via 19 mechanical invariants (I1-I19) covering state validity, slug uniqueness, UID format, PDF path normalization, file presence on disk, sha256 integrity, page-1 validation log coherence, state history monotonicity, attempt numbering, blocked-reason

• sota-auditor

  Final authority on the truthfulness of references cited in State-of-the-Art reviews and academic papers. Activate this skill whenever the session involves auditing, correcting, or cleaning citations in a SOTA or article, or when responding to verdicts from `pdf-cascade` / `registry-doctor`. Triggers

• sota-writer

  Write structured State-of-the-Art (SOTA) reviews / literature reviews for academic research projects with **zero hallucinated citations**. Activate this skill whenever the user wants to write, update, or expand a SOTA. Triggers (FR + EN) : "écris un SOTA", "état de l'art sur", "revue de littérature"

Slash commands (22)

• /paper-trail:paper-trail-acquire

  Troisième passe du pipeline cible refondu. Lance la cascade PDF (10 sources : Crossref OA + arXiv + OpenAlex + Unpaywall + HAL + CORE + éditeur par DOI + archive.org + WebSearch ; jusqu'à 17 avec les voies par navigateur et les sources étendues opt-in) ciblée sur les refs d'un SOTA donné. Différent

• /paper-trail:paper-trail-audit-all

  Batch audit of every SOTA in the vault. For each SOTA, identifies refs that are page1_validated (technical OK) but not yet sota_cited_confirmed (content audited), and launches audit-sota on those SOTAs. Returns a per-SOTA summary at the end.

• /paper-trail:paper-trail-audit-article

  Per-citation audit of an academic article (LaTeX or Markdown). Produces RECEIPTS.md classifying each citation as VALID/ADJUST/INVALID/UNVERIFIABLE. Optional --warn inserts inline warnings in a .bak copy of the source.

• /paper-trail:paper-trail-audit-sota

  Audit a SOTA's bibliography. Classify each cited ref by validation state. Optional --purge removes citations to retracted refs from the SOTA (with .bak backup).

• /paper-trail:paper-trail-cascade

  Acquire PDFs via the 8-source cascade (11 with opt-in extended sources) for a single ref by slug, or a batch filtered by state. Validates page 1 anti-homonymy on each download.

• /paper-trail:paper-trail-decide

  Inspect a single reference in detail (identity, PDF status, acquisition history with verdicts, citation context in vault, state transitions) and decide its fate. Offers actionable decisions based on the ref's current state.

• /paper-trail:paper-trail-doctor

  Audit the registry via the 19 mechanical invariants (I1-I19). Reports ERROR/WARN/INFO violations. Optional auto-fix for safe ones (I4 path, I6 sha256, I9 attempts).

• /paper-trail:paper-trail-identify

  Première passe du pipeline cible refondu (read-only). Produit un rapport d'identification : pour chaque mention citée dans le SOTA, indique si la fiche existe déjà au registre, son état actuel, si elle a un PDF, et l'action recommandée (réutiliser / créer / passer en revue). Ne modifie ni le SOTA ni

• /paper-trail:paper-trail-ingest-all

  Batch INGEST across the entire vault. Scans all SOTAs, identifies those with bibliographic sections containing free-text citations, then runs /paper-trail:ingest on each one sequentially. Reports per-SOTA summary at the end. The single batch entry point to make a legacy vault fully conform to the pa

• /paper-trail:paper-trail-ingest

  Ingest the citations of one SOTA into the registry. Extracts bibliographic sections, parses citations via the citation-parser sub-agent, resolves DOI via Crossref/S2, deduplicates against the registry, creates new candidate refs, and substitutes free-text citations with [[wikilinks]]. Required first

• /paper-trail:paper-trail-inject-url

  Injecte une URL OA connue (HAL, dépôt uni, NIME, page perso) pour une ref dont la cascade automatique a échoué, puis relance l'acquisition + validation page 1.

• /paper-trail:paper-trail-linkify

  Dernière passe du pipeline cible refondu. Insère les wikilinks finaux dans le SOTA (vers PDF si validé, sinon vers ancre dans une section `## Statut des sources` régénérée idempotemment en bas du fichier). Présuppose que les passes identify/purge/acquire ont été lancées.

• /paper-trail:paper-trail-new-paper

  Start writing an academic paper (IMRaD structure) on a topic, with anti-hallucination citation verification at every step. Builds on existing audited SOTAs.

• /paper-trail:paper-trail-new-sota

  Create a new State-of-the-Art review on a topic, guaranteed without hallucinated citations. Inverted workflow (research → acquire PDFs → read → write), refuses to write from memory.

• /paper-trail:paper-trail-purge

  Nettoie les wikilinks invalides d'un SOTA (vers refs retracted, refs `_0000_*` orphelines, suffixes numériques `_2_3_4`, fichiers techniques `20_ATLAS/`, `30_DEV/`, `.canvas`, slugs non-bibliographiques). Opère uniquement sur le SOTA, jamais sur le registre. Backup git auto avant `--apply`.

• /paper-trail:paper-trail-reactivate-ocr

  Re-evaluate refs in state `awaiting_rtfm_ocr` via `rtfm check`. Transitions to `page1_validated` if OCR succeeded, or `needs_reacquisition` if OCR failed.

• /paper-trail:paper-trail-receipts

  Local-only per-citation audit (no remote API). Reads the cited PDFs from the local registry, generates RECEIPTS.md. Faster than audit-article (no Crossref / paper-search calls).

• /paper-trail:paper-trail-registry-cleanup

  Nettoyage historique du registre des fiches bibliographiques (les ~900 fiches existantes). Cible les vieilles fiches mal nommées (`*_0000_*`, `_untitled`) ET les duplicates avec suffixes numériques (`foo_2020_bar_2`, `_2_3_4`) qui sont des artefacts de runs INGEST passés. Délègue les décisions au su

• /paper-trail:paper-trail-resolve-textbooks

  Resolve incomplete textbook references in the registry. Reads candidates via `pipeline resolve-textbooks --list`, invokes the `textbook-resolver` sub-agent to produce a decisions JSON (merge_into / complete / blocked), and applies via `pipeline resolve-textbooks --apply-from`. Fully automated cleanu

• /paper-trail:paper-trail-review

  Review and arbitrate problematic references (cascade-exhausted, unresolved UID, awaiting OCR). Generates an up-to-date report, walks through cases by category, and applies arbitration decisions to the registry.

• /paper-trail:paper-trail-search

  Search the validated registry for references matching a topic (author, title, year, slug). Returns only refs in state page1_validated or sota_cited_confirmed by default — i.e. references that have been technically validated (PDF acquired, page 1 OK) or fully audited (content validated against PDF).

• /paper-trail:paper-trail-status

  Show the registry status — count of refs per FSM state. Read-only, fast (< 5s).

Subagents (6)

• cascade-runner

  Sub-agent that orchestrates the PDF acquisition cascade for a batch of refs. Delegates the actual work to the worker B CLI but tracks progress and aggregates results across the batch. Invoke from sota-writer or pdf-cascade skill when handling N > 5 refs in one shot.

• citation-parser

  Sub-agent that parses bibliographic sections and inline citations from SOTA / article text. Takes raw text (a section header + content, or an inline excerpt) and returns structured JSON `[{author, year, title, doi?, venue?, raw}]`. Isolates the LLM extraction from the main agent context. Invoke from

• claim-checker

  Sub-agent that audits a specific claim against the PDF cited. Invoked by citation-receipts skill for deep PDF↔claim verification. Returns structured verdict (VALID/ADJUST/INVALID/UNVERIFIABLE) with evidence quoted from the source. Isolates the heavy PDF reading from the main agent's context.

• page1-validator

  Sub-agent that validates whether a downloaded PDF matches the expected metadata (author, title, year). Anti-homonymy check on page 1. Invoke when a manual page 1 verification is needed on an acquired PDF, separate from the cascade's automatic validation.

• researcher

  Sub-agent that performs exhaustive multi-source academic search (paper-search MCP across 22 platforms + optional NotebookLM + optional WebSearch). Returns structured JSON of candidate refs for sota-writer phase A. Invoke when broad literature search is needed without polluting the main agent's conte

• textbook-resolver

  Sub-agent that decides what to do with incomplete textbook references in the registry. Takes a JSON list of candidates (refs with year=0000 or title=empty, plus their siblings = other refs with same lastname) and returns JSON decisions (merge_into, complete, or blocked). Invoked by /paper-trail:reso

Hooks (5)

• PreToolUse

  python3 "${CLAUDE_PLUGIN_ROOT}/tools/precheck_sota_wikilinks.py"

• PreToolUse

  python3 "${CLAUDE_PLUGIN_ROOT}/hooks/pre_save_sota_check.py"

• PostToolUse

  python3 "${CLAUDE_PLUGIN_ROOT}/hooks/post_edit_ref_check.py"

• PostToolUse

  python3 "${CLAUDE_PLUGIN_ROOT}/hooks/post_edit_sota_check.py"

• SessionEnd

  python3 "${CLAUDE_PLUGIN_ROOT}/hooks/session_end_doctor.py"

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