ResearchTools — Manual

Purpose

Ask for my book (French version): Vibe Design. 30$ contribution via:

ResearchTools is an AI-assisted toolbox for researcher-professors and graduate students who want to find and fix the issues hiding in their academic writing before a reviewer, a thesis committee, or a grant panel does. It contains two loop for authoring and coding. It covers the whole process: starting a literature review, auditing an existing review, a complete paper, a UQAC thesis or thesis proposal, cleaning/improving a BibTeX file, helping to respond to peer reviewers, checking submission readiness against a target journal, building the submission package, and converting Word to LaTeX with high accuracy.

Every check is grounded in the same working norms: no reference enters a document without being validated against Scopus (no fabricated citations, no invented DOIs), weaknesses are reported as actionable findings with an executable improvement plan rather than vague encouragement, and drafts pass a multi-model deliberation (Gemini + GitHub Copilot debate, arbitrated with Claude) before a plan or review is finalized. Each improvment is evaluated with a score and then you can see the quantitative improvments.

The toolbox is built as agents, skills, and commands for Claude Code, with generated mirrors for GitHub Copilot, OpenCode, Continue, and Aider (see Installation). Typical entry points: /litreview for a new topic (review update using \litreview-updater), /auditpaper before submitting, /auditthesis before a defense, /bibclean on any .bib file, /replyreviewer when the reviews come back.

TODO in 2026

1- Agent paper2talk (latex paper to a talk for a conference using some parameters such as time 10 to 12 minutes) for conference (september 2026).

2- Agent thesis2defence (latex thesis to defence talk in Beamer, 30 to 45 minutes), october 2026.

3- Thesis-Tracker: full UI/UX with user login, database, to fill paperworks, forms, track paper submission process, manage mindmap to create new paper ideas, end of 2026. We need to investigate if we use n8n, or other agents over a cloud or local on a server.

About this manual

Reference for the skills, agents and commands shipped in this repository. Everything documented here lives under .claude/ in this repo (academic research tooling for LaTeX writing, Scopus reference validation, paper/thesis auditing, and grant-template conversion). For a map of how the pieces relate, see Architecture.md.

The repo ships 11 skills, 16 agents, and 21 commands.

Installation

Follow these steps on any machine after cloning the repository.

Install scripts overview

Three scripts, three different jobs and lifecycles. setup.ps1 is the single entry point: it wraps the other two via -InstallJunctions / -InstallTools, and -All runs the full sequence (config, then junctions, then tools) in one pass.

	`setup.ps1`	`install-junctions.ps1`	`install.ps1`
Job	Generate machine-local config: `.claude\settings.json` + `CLAUDE.md` from templates (detects Git Bash, Node, Obsidian paths of THIS machine)	Link the repo into `~/.claude` so Claude Code loads agents/skills/rules/commands in every workspace	Generate mirrors for other coders: GitHub Copilot, OpenCode, Continue, Aider (`-Personal` adds the user-level Copilot install)
Output	2 machine-specific files (paths differ per PC)	Links in `C:\Users\<you>\.claude\`	Generated files committed in the repo (`.github\`, `.opencode\`, `.continue\`, `CONVENTIONS.md`) + optional user copies
When to run	Once after clone (or when machine paths change)	Once after clone; re-run when an agent or skill is ADDED (or a hardlink detached after a pull)	After every agent/command/rule EDIT, then commit the output
Privilege	none	symlinks want Developer Mode (automatic hardlink fallback)	none
Interactive	yes (asks vault path, confirms)	no	no
Via `setup.ps1`	-	`-InstallJunctions`	`-InstallTools`

.\setup.ps1 -All -Personal   # new machine: config + Claude links + all tool mirrors

Prerequisites

Tool	Required for
Claude Code	Running agents and slash commands
Git for Windows (includes Git Bash)	Hooks that use `bash` shell
Node.js	Caveman-mode hooks (`caveman-activate.js`, etc.)
Python 3.x	Scopus skill scripts + security hooks (`betterleaks`, `pip-audit`, `prompt-injection-defender`)
`pip install requests google-genai openai`	Scopus skill + Gemini/Copilot cross-review
`pip install pymupdf4llm pymupdf` (optional, AGPL-3.0)	`extract-statistic` skill PDF parsing (`mine` mode), LLM-ready Markdown + table extraction; reuses `SCOPUS_API_KEY` via `download_pdf.py`, needs no key of its own
`pip install docling markitdown[pdf]` (optional, MIT; Docling pulls torch)	Pluggable Markdown backend for `extract_text.py` (`--stats-scan` / `--section-scan`) and HTML conversion in the any-format retrieval path. Docling is the default (best tables/layout), MarkItDown the light fallback; absent both, the parser uses pymupdf4llm + a tag-strip
`pip install matplotlib` (+ optional `folium`)	`geolocalisation` skill: world-map PNG figure (`matplotlib`) and interactive HTML map (`folium`). No geopandas/GDAL. The `--full-text` study-site scan additionally reuses `pymupdf` + `download_pdf.py`
`pandoc`	`word2latex` skill (Word → LaTeX)
`pdflatex` (TeX Live / MiKTeX)	`recommendation-letter` skill: compile letters to PDF (degrades to `.tex` only if absent)
Obsidian Desktop (optional)	Obsidian vault integration in `CLAUDE.md`

Step 1 — Clone the repository

git clone https://github.com/LARi-UQAC/ResearchTools.git
cd ResearchTools

Step 2 — Generate machine-local configuration

Run the setup script from the repository root. It auto-detects Git Bash and Node.js, asks for your Obsidian vault path (optional), and generates two gitignored files: .claude/settings.json and CLAUDE.md.

.\setup.ps1

Verify that no {{placeholder}} remains after the script completes — it reports any unreplaced values in the validation step.

Step 3 — Make agents available globally (optional, recommended)

This step links ~/.claude/agents/, ~/.claude/skills/, ~/.claude/rules/, and ~/.claude/commands/ into this repository, so that Claude Code loads these agents and skills in every workspace, not only when you open this folder.

Only missing links are created; existing ones are never overwritten.

# Preview what will be created without making changes
.\setup.ps1 -InstallJunctions -Preview

# Apply
.\setup.ps1 -InstallJunctions

Alternative (direct): .\install-junctions.ps1 (or .\install-junctions.ps1 -WhatIf to preview).

How linking works by directory type (skills are folder-based, agents are file-based — see the Agents section):

Directory	Link type	One link per…	New file/folder after `git pull`
`agents/`	SymbolicLink per FILE (HardLink fallback when Developer Mode is off)	Agent file (e.g. `scopus-researcher.md`)	Re-run `.\setup.ps1 -InstallJunctions` — existing agents show `[EXISTS]`, only the new one is created. With HardLinks, also re-run after a pull that EDITS an agent (git rewrites detach hardlinks)
`skills/`	Junction per sub-folder	Skill (e.g. `scopus/`)	Re-run — only the new skill is created
`rules/`	Junction on the whole directory	Entire `rules/` folder	Automatic — new `.md` files are visible immediately through the existing junction, no re-run needed
`commands/`	Junction on the whole directory	Entire `commands/` folder	Same as above

Junctions need no Administrator privileges. Agent file links prefer SymbolicLinks (enable Windows Developer Mode, or run elevated); without that privilege the script falls back to HardLinks automatically.

Fallback when rules/ or commands/ already exists as a real directory (another project previously created it): the script automatically switches to per-file symbolic links for any missing files. If Administrator privileges are required for the symlinks, the script re-launches itself elevated.

Because the links point directly into this repository, a git pull is all that is needed to propagate rule and command improvements contributed by any collaborator.

Step 4 — Install for other coding tools (optional)

install.ps1 regenerates the GitHub Copilot, OpenCode, Continue, and Aider mirrors from the canonical .claude/ sources (agents, task commands, rules). With -Personal it also installs the Copilot agents to ~/.copilot/agents/ and the prompt/instruction files to the VS Code user profile, making them available in every workspace:

.\install.ps1                     # repo-level mirrors only (commit the output)
.\install.ps1 -Personal           # + user-level Copilot install
.\install.ps1 -Profile cosmetic   # + select the active domain profile
.\setup.ps1 -InstallTools -Personal   # same, via the setup entry point

install.ps1 also records the active domain profile (see Profiles): pass -Profile <name> or answer the interactive prompt; non-interactive runs keep the current default (engineering).

Details in Using the agents outside Claude Code.

Contributing improvements

Fork the repository, improve an agent or skill on a feature branch, and open a pull request against main. The repository owner reviews and merges; a git pull on their machine immediately updates the linked entries via the junctions.

To add or edit an agent, skill, or command (and propagate it to Copilot, OpenCode, Continue, and Aider), follow the turnkey guide docs/authoring-and-mirrors.md: canonical sources, per-type checklist, and the install.ps1 mirror regeneration. Shared project conventions and environment facts (English-only definition files, agent/skill layout, local-model routing, git/GitHub workflow) live in docs/contributor-notes.md.

Profiles

A domain profile centralizes everything domain-specific (Scopus subject areas and exclusions, topical-relevance signals, off-topic flag, stats profile, author, course context, language) in one YAML file under profiles/, so the agents and skills stay shared across users and labs: one maintained core, N profiles.

Profile	Domain	Author	Default
`engineering.yaml`	Mechanical / electrical / ML / control / systems engineering	Martin Otis (UQAC)	yes
`cosmetic.yaml`	Cosmetic / formulation science (SPF, microbiome, dermatology, sensory)	Lionel Ripoll (UQAC)	no
`_template.yaml`	Copy it to `profiles/<domain>.yaml` to add a new domain	-	-

The active profile is recorded in .claude/CLAUDE.md as the machine-readable line active_profile: <name>. Select it at install time (.\install.ps1 -Profile <name>, or the interactive prompt) or edit that line directly. Currently wired consumer: scopus-researcher (search clauses, Step 3a relevance check, synthesis framework); the remaining fields (author, stats_profile, course_context, language) are schema-ready and will be wired incrementally. Field-by-field spec, fallback rules, and the add-a-profile procedure: profiles/README.md.

Environment variables / API keys

Set these at the Windows User scope (PowerShell), then restart Claude Code:

[System.Environment]::SetEnvironmentVariable('SCOPUS_API_KEY', 'your-key', 'User')

Variable / source	Required for	Where to get it
`SCOPUS_API_KEY`	Required — all `/scopus`, `/auditreview`, `/auditpaper`, `/auditthesis`, `/litreview`, `/litreview-updater`, `/bibclean`, `/replyreviewer`, and PDF retrieval	Elsevier Developer Portal
`.scopus_key` file	Fallback for `SCOPUS_API_KEY` — place the key in `.claude/skills/scopus/.scopus_key` (gitignored)	same key as above
`UNPAYWALL_EMAIL`	Optional — enables the Unpaywall open-access tier in `download_pdf.py` (HTML/PDF fallback when no publisher PDF); a plain contact email, or pass `--email`	any institutional email
`GEMINI_API_KEY`	Optional — Gemini 2.0 Flash cross-review and table enrichment (deliberation panel)	Google AI Studio
`GITHUB_TOKEN`	Optional — GPT-4o cross-review via GitHub Models (deliberation panel)	GitHub → Settings → Developer settings → Personal access token
`S2_API_KEY` (or `SEMANTIC_SCHOLAR_API_KEY`)	Optional — Semantic Scholar author/PDF backfill; without it the throttled public pool is used	Semantic Scholar API key request
`--insttoken` (CLI flag, not an env var)	Optional — off-campus Elsevier access when not on the UQAC network/VPN	UQAC library / Elsevier institutional token

An on-campus network connection or active UQAC VPN is required for Scopus access unless an --insttoken is supplied. Secrets are kept out of git: .env, secrets/, and credentials/ are listed in .gitignore.

Token Management

Use these tools together to keep sessions fast and cheap.

Output modes

Mode	Command	Max length	Formatting
Normal	(none)	Unlimited	Full — headers, tables, bullets
Concise	`/concis`	5 sentences	Structured bullets allowed
Slim	`/slim`	2 sentences	Code blocks only, no prose

Recommended workflow

Start every session with /slim (quick tasks) or /concis (exploratory work)
Scope context with /focus <topic> to avoid loading irrelevant files
Monitor with /ctx when responses feel slow — it reports context pressure in under 10 lines
Compress with /compact when /ctx reports moderate or high pressure

/compact is destructive — conversation history is summarized and cannot be restored. Always run /ctx first to confirm it is needed.

Quick reference

Command	When to use
`/slim`	Fast edits, one-liners, quick questions
`/concis`	Code reviews, multi-step explanations
`/focus <topic>`	Long sessions touching many files
`/ctx`	When the session feels sluggish or heavy
`/compact`	After `/ctx` reports moderate/high pressure

Skills

Skills bundle scripts and references the agents reuse. Eleven ship in this repo.

Skill	Purpose	Entry point
`scopus`	Search Scopus, validate references, fetch PDFs via the Elsevier REST API (with a Semantic Scholar fallback).	`/scopus`, `.claude/skills/scopus/SKILL.md`
`scientific-writing`	Core writing skill: scientific manuscripts in flowing IMRAD prose with verified citations (IEEE/APA/AMA/Vancouver) and reporting guidelines (CONSORT/STROBE/PRISMA).	`.claude/skills/scientific-writing/SKILL.md`
`scholar-evaluation`	ScholarEval framework — scores research work across problem formulation, literature review, methodology, data, analysis, results, writing, citations.	`.claude/skills/scholar-evaluation/SKILL.md`
`deliberation`	Two-round Gemini ↔ GitHub Copilot debate over a near-final draft; Claude arbitrates and validates any new references against Scopus. Used inside the auditor/researcher agents.	`.claude/skills/deliberation/SKILL.md`
`extract-statistic`	Statistical analysis. Mode `audit`: review a manuscript's own statistics (test selection, assumptions, effect size, presentation, cross-validation). Mode `mine`: extract the reported statistics of a corpus's full-text PDFs and synthesize a corpus statistics table plus an improvement-opportunity list. Engineering-default domain profiles. Used inside `paper-auditor` / `thesis-auditor` (audit) and `scopus-researcher` (mine).	`.claude/skills/extract-statistic/SKILL.md`
`extract-futureworks`	Future-works analysis (reuses `extract_text.py --section-scan`). Mode `audit`: review a work's own future works (presence, testability, link-to-limitation, novelty) and validate its hypotheses against the cited-corpus future works, proposing stronger ones. Mode `mine`: extract every corpus paper's stated future works, build a review-fit table, Pareto 80/20-rank it (low effort, high impact first), and emit a research-opportunity list. Used inside the four auditors (audit) and `scopus-researcher` (mine), where it is a hard gate: no hypothesis/project without it.	`.claude/skills/extract-futureworks/SKILL.md`
`word2latex`	Convert a Word `.docx` template (Mitacs, CRSNG, FRQNT, UQAC, partner forms) into a faithful LaTeX source. Delegates the patch work to the `word-to-latex` agent.	`/word2latex`, `.claude/skills/word2latex/SKILL.md`
`drawio2tikz`	Convert one `.drawio` sheet into a coordinate-exact TikZ fragment (absolute coordinates, edge anchoring, braces, rotation, FR→EN `--translate`). The sanctioned absolute-coordinate exception to the hand-authored TiKZ rules.	`/drawio2tikz`, `.claude/skills/drawio2tikz/SKILL.md`
`geolocalisation`	Map a review corpus in space from its `.bib`: resolve each paper's study/case-study site (per-DOI Scopus abstract + title + keywords, optional `--full-text` PDF scan via `download_pdf.py`, matched against an offline Natural Earth gazetteer), write a reviewable draft table with a confidence column and a per-paper provenance note, then render CSV, KML (Google My Maps), GeoJSON (QGIS/Leaflet), a world-map PNG, an interactive HTML map, and a per-country count table. Human-reviewed; an override CSV always wins.	`/geolocalisation`, `.claude/skills/geolocalisation/SKILL.md`
`loop-engineer`	Budget-bounded develop-and-improve loop (Agent SDK driver): design → plan → code → comment → test → review → score → correct, looping until a composite gate (tests green, no CRITICAL/HIGH, score `>=` min) or a hard budget/max-iters/no-progress stop. Fable 5 orchestrates; Opus/Sonnet act; `local-coder`/`local-writer` do local generation. `loop_audit.py` aggregates the installed reviewers into a 0-100 score with a security hard floor; merge to a protected branch is human-gated.	`/loopdev`, `.claude/skills/loop-engineer/SKILL.md`
`recommendation-letter`	Generate support, recommendation, appreciation, acceptance, and dispense (short-stay invitation) letters in LaTeX → PDF from a candidate's files. Two tracks: Claude authors the four persuasive types (fr/en); a stdlib-only Python script fills the fixed French acceptance/dispense forms (candidate status, funding provider, 120-day work-permit exemption, paired output). Sample data is synthetic.	`/recommendation-letter`, `.claude/skills/recommendation-letter/SKILL.md`

`/scopus` — Scopus academic search

Searches the Scopus database via the Elsevier REST API. Requires SCOPUS_API_KEY (see the API-keys table above) and an active institutional network connection (campus or VPN), or an --insttoken.

Command	What it does
`/scopus <topic>`	Search top papers on a topic
`/scopus review <topic>`	Structured literature review with inline citations
`/scopus validate <DOI or title>`	Confirm a reference exists and return full metadata
`/scopus cite <DOI>`	Citation count + full metadata for one paper
`/scopus author <name>`	Author h-index and top publications
`/scopus journal <name or ISSN>`	Journal SJR quartile, CiteScore, subject areas

Files:

.claude/skills/scopus/SKILL.md
.claude/skills/scopus/scripts/scopus_api.py — Scopus REST client
.claude/skills/scopus/scripts/semantic_scholar_api.py — Semantic Scholar fallback
.claude/skills/scopus/scripts/download_pdf.py — any-format full-text retrieval (PDF, else HTML/Markdown via Unpaywall, arXiv, PMC, validated DOI landing), plus an opt-in --browser tier
.claude/skills/scopus/scripts/browser_fetch.py — tier 8: a real Playwright Chromium for challenge-gated publishers (Akamai/Cloudflare), with a per-paper refs/_sources.json override URL (e.g. ResearchGate) for papers with no institutional access; optional (needs playwright + playwright install chromium)
.claude/skills/scopus/scripts/litreview_update.py — incremental-update bookkeeping for /litupdate (baseline fingerprint, delta dedup via bib_batch.title_match, dated output paths, CHANGELOG scaffold)
.claude/skills/scopus/scripts/gemini_reviewer.py · github_reviewer.py · gemini_table.py — cross-review cores

`geolocalisation` — corpus study-location mapping

Turns a corpus .bib into a spatial map of where each paper's empirical study was conducted. A case-study site is not a bibliographic field (no API returns it — it lives in the text), so the skill is deliberately human-in-the-loop: it emits a draft with a confidence column and a per-paper provenance note, a human reviews it, and a manual override CSV always wins before rendering. Requires SCOPUS_API_KEY (campus network or VPN), or run --no-scopus for a manual-entry template.

Stage	Command	Output
1 — extract	`extract_locations.py --bib <corpus.bib> --out <dir> [--full-text] [--override <curated.csv>]`	`study_locations.csv` (with `confidence`, `evidence_field`, `evidence`, `provenance`) + `provenance/<citekey>.md` audit notes
2 — review	(human)	curate / confirm; correct every `low`/`none` row via the override CSV
3 — render	`generate_geomap.py --csv <dir>/study_locations.csv --out <dir> [--formats …] [--min-confidence …]`	CSV, KML (Google My Maps), GeoJSON (QGIS/Leaflet), world-map PNG, interactive HTML, `country_counts.csv`

Extraction: per-DOI Scopus abstract + title + keywords; place names matched against an offline Natural Earth gazetteer, with capitalization + a population floor + a common-word stoplist for precision (separates the city Mobile from the word mobile).
--full-text: for none/low results, downloads the PDF via the scopus skill's download_pdf.py, reads it with PyMuPDF, and scans only study-cue sentences with affiliation lines rejected — an unfiltered full-text scan maps author affiliations, not study sites. Adopted only when it beats the abstract; PDFs cached in refs/.
Auditability: every mapped point carries evidence_field + the verbatim evidence sentence in the CSV, a provenance/<citekey>.md note, and the same surfaced in the HTML popup, GeoJSON properties, and KML description.
No geopandas/GDAL — the basemap is drawn from raw GeoJSON. Deps: matplotlib (PNG), optional folium (HTML) and PyMuPDF (--full-text).

Files:

.claude/skills/geolocalisation/SKILL.md
.claude/skills/geolocalisation/scripts/extract_locations.py — bib + Scopus/full-text → draft CSV + provenance notes
.claude/skills/geolocalisation/scripts/generate_geomap.py — reviewed CSV → CSV/KML/GeoJSON/PNG/HTML + per-country table (no geopandas)
.claude/skills/geolocalisation/references/geocoding-protocol.md — extraction method, confidence rubric, override format, full-text pipeline
.claude/skills/geolocalisation/scripts/Test/test_extract_locations.py — offline unit tests (bib parse, matcher, evidence, full-text)

recommendation-letter — support / recommendation / acceptance / dispense letters

Generates letters in LaTeX → PDF for Prof. Otis / LAR.i from a candidate's own files. Two tracks: Claude authors the four persuasive types (scholarship, academic_position, industry_position, appreciation; French or English), while a standard-library-only Python script fills the fixed French acceptance and dispense forms. candidate_status (applicant / current_student / graduated) sets how the candidate is named; funding_provider (supervisor / candidate / combination) branches the funding paragraph; the dispense letter carries the < 120-day work-permit exemption paragraph and warns when a stay exceeds it; invitation_pair=both emits the acceptance and dispense letters together. A style-hygiene linter enforces the AI-usage rules. All shipped sample data is synthetic.

Files:

.claude/skills/recommendation-letter/SKILL.md
.claude/skills/recommendation-letter/scripts/generate_letter.py — two-track assembler, validator, pdflatex compile
.claude/skills/recommendation-letter/scripts/letter_templates.py — preamble, letterhead/signature, acceptance/dispense French templates
.claude/skills/recommendation-letter/scripts/Test/test_generate_letter.py — offline unit tests (53 cases)
.claude/skills/recommendation-letter/references/quality-patterns.md — authored-track quality patterns
.claude/skills/recommendation-letter/evals/ — synthetic sample configs

Security audit (SkillSpector)

All eight skills under .claude/skills/ were scanned with SkillSpector v2.2.3 in static-only mode (skillspector scan <skill> --no-llm) on 2026-06-18, every dependency finding cross-checked against pip-audit.

True positives — corrected

LP3 (missing permission declaration): added to the frontmatter of scopus, deliberation, extract-statistic, scholar-evaluation, word2latex, and drawio2tikz a per-skill permissions: list declaring exactly the capabilities each skill's scripts use (e.g. scopus → [env, read, write, network]), plus an allowed-tools: [Read, Write, Edit, Bash] runtime restriction. Re-scan confirms LP3 cleared with no LP1/LP4 regression.
SC1 (unpinned dependencies): pinned >= to exact == versions in scopus/scripts/requirements.txt (requests, google-genai, openai) and extract-statistic/scripts/requirements.txt (pymupdf4llm, pymupdf, docling, markitdown), using versions confirmed clean by pip-audit.

False positives — reviewed and ignored

SC4 (vulnerable dependency): flagged by package name only; pip-audit resolves every declared >= floor to a patched release (No known vulnerabilities found).
E1 / E2 (external transmission / env harvesting): skills reading their own configured API keys and querying their own research APIs (Elsevier, Unpaywall, Semantic Scholar).
TT2 (taint flow): the https-only, redirect-disabled PDF download in download_pdf.py.
PE3 / RA2 / EA1 / EA2 / P6: keyword matches inside docstrings/markdown (e.g. SNIPList, the GITHUB_TOKEN doc line, a **…tool:** bullet, a DOI-workflow description, a returned local prompt string).
AST4 (subprocess): the test harness invoking the skill script with a fixed argument list.

scientific-writing and extract-futureworks required no changes.

The geolocalisation skill was added after this scan (2026-07) and should be scanned on the next pass. Its declared dependencies pin exact/floor versions verified with pip-audit: matplotlib==3.9.2, pillow>=12.3.0 (fixes PYSEC-2026-2253..2257), and the optional folium==0.17.0 / PyMuPDF==1.27.2. It declares permissions: [read] and allowed-tools: [Read, Write, Edit, Bash], reuses the scopus skill's network I/O through download_pdf.py rather than opening its own, and fetches only public-domain Natural Earth basemaps (TLS-verified, cached).

Commands (Slash Commands)

Invoked with /command-name [arguments] in any Claude Code session. All files live in .claude/commands/.

Command	What it does	Arguments
`/concis`	Concise mode for the rest of the session	No
`/slim`	Slim mode — ultra-minimal output (2 sentences, code only)	No
`/focus <topic>`	Scopes the session to one topic only	Yes — topic
`/ctx`	Audits context-window pressure (turns, topics, recommendation)	No
`/tikz [code]`	Validates TiKZ code against 6 rules (anchoring, arrows, overlaps…)	Optional — code or file
`/test [module]`	Runs project tests following `.claude/rules/testing.md`	Optional — module/file
`/doc <target>`	Generates or updates documentation for a file or function	Yes — file/function
`/latex [args]`	Diagnoses and fixes LaTeX errors from the `.log` or open file	Optional — specific error
`/ref <citation>`	Formats and validates an academic reference (UQAC/LAR.i style)	Yes — reference
`/litreview <topic>`	Full autonomous literature review: search → validate → synthesize → comparison table → hypotheses + contributions → objectives → context → novelty checklist	Yes — research topic
`/litupdate <review.tex>`	Incrementally update an existing review with new papers: windowed search → delta dedup → validate/grade → preemption check (deliberation + scholar-evaluation) → dated `\added{}` copy `_up_YYYYMMDD.tex` + CHANGELOG. Schedulable (draft + REVIEW REQUIRED when unattended)	Yes — existing review `.tex`
`/auditreview [file or text]`	Audit an existing review: validate references, flag errors, novelty checklist, executable improvement plan	Optional — file/text/IDE file
`/auditpaper [file or text]`	Audit a complete paper: references, methodology, results, discussion, future works — Scopus validation + cross-review + improvement plan	Optional — file/text/IDE file
`/auditthesis [main.tex or dir]`	Full UQAC thesis audit: front matter, jury, hypothesis flow, chapter structure, references, figures, equations, acronyms, LLM-style, bilingual résumé/abstract, UQAC formatting	Optional — path/dir/IDE file
`/bibclean [file.bib]`	Clean and validate a BibTeX file: required fields, author normalization, duplicates, DOI enrichment, SJR quartile, publisher approval check	Optional — `.bib` file/IDE file
`/submitcheck <file.tex> <journal>`	Check submission readiness for a target journal: page count, sections, reference style, abstract length, keywords, anonymization	Yes — `.tex` file + journal
`/replyreviewer`	Point-by-point LaTeX response letters + track-change markup in the paper via the `changes` package (one letter per reviewer file)	Yes — see below
`/word2latex`	Convert a Word `.docx` template to a faithful LaTeX source (pandoc + standard patch sequence)	Yes — `.docx` path
`/geolocalisation`	Map a review corpus's study locations from its `.bib`: draft study-location table (confidence + per-paper provenance), human review, then CSV/KML/GeoJSON/PNG/HTML + per-country count. Optional `--full-text` PDF scan.	Optional — `.bib` file/dir/IDE file
`/recommendation-letter`	Generate a support / recommendation / appreciation / acceptance / dispense letter in LaTeX → PDF from a candidate's files (two tracks; candidate status + funding provider; paired invitation).	Optional — folder / paths / IDE file

`/concis` — Concise mode

Activates for the rest of the session: max 5 sentences for short answers, structured bullets for long answers, no preamble, no trailing summary, code written directly with WHY-only comments. Responds in French unless the active file is in English.

File: .claude/commands/concis.md

`/focus <topic>` — Session scope

Restricts the session to a single topic; everything outside it is ignored. Responds in French unless the active file is in English.

File: .claude/commands/focus.md

`/ctx` — Context window audit

Reports, in under 10 lines: estimated exchange turns, top 3 context-consuming topics/files, a low/moderate/high pressure level, and a /compact recommendation when needed. Reads no additional files. Responds in French.

File: .claude/commands/ctx.md

`/tikz` — TiKZ validation

Validates TiKZ code (from $ARGUMENTS or the IDE file) against 6 rules:

Rule	What is checked
Line breaks in nodes	`align=center` only — never `text centered`
backgrounds + scaling	No `\begin{scope}[on background layer]` inside `\resizebox`/`\scalebox`
Arrow angles	Arrows connect perpendicularly to node borders (.north/.south/.east/.west)
Overlaps	Min 3-character gap between rectangles; arrow labels must not overlap geometry
Anchoring	`positioning` library + `node distance` only — no absolute coordinates
TiKZiT compatibility	Named styles in `.tikzstyles`; no exotic libraries

For each violation: cites the line, explains the cause, provides corrected code directly.

A figure generated by the drawio2tikz skill is exempt from the Anchoring and TiKZiT-compatibility rules (it uses absolute coordinates by design); arrow tips, spacing, and overlaps are still checked.

File: .claude/commands/tikz.md

`/test [module]` — Run project tests

Reads .claude/rules/testing.md, selects the correct venv, runs the tests, and reports passed / total with short error messages and likely causes.

File: .claude/commands/test.md

`/doc <target>` — Documentation generator

Generates documentation following .claude/rules/code-style.md (Python Stage-N module + Purpose/Inputs/Outputs docstrings; C# /// <summary>; LaTeX/Markdown equation formatting). Documents WHY, not WHAT. Responds in French unless the active file is in English.

File: .claude/commands/doc.md

`/latex` — LaTeX diagnosis and fix

Reads out/*.log first for exact error lines, cites the line, explains the cause, and applies the fix directly. Priority checks: \resizebox wrapping a backgrounds-library tikzpicture, \\ in a text centered node, \addcontentsline order. States whether a two-pass recompilation is needed. Responds in French.

File: .claude/commands/latex.md

`/ref <citation>` — Academic reference formatter

Formats and validates references per UQAC / LAR.i rules.

Accepted publishers: IEEE, Springer, Elsevier, Taylor & Francis, Cambridge, Wiley, IET, IOP, ACM, MDPI, ASME, ACME, BioMed Central (BMC). Any other publisher requires professor approval. Provides: full LaTeX reference, clickable DOI via \href, a 0–100 % confidence level with justification, and an introductory sentence. Never fabricates a reference or DOI.

File: .claude/commands/ref.md

`/replyreviewer` — Peer reviewer response generator

Generates a formal LaTeX response letter per reviewer comment file and applies track-change markup directly in the paper using the changes package. The reviewer ID (id=RN) in each \added, \replaced, or \deleted command is the permanent, visible link between the paper modification and the response letter. Delegates to the reviewer-response agent.

Full command syntax:

/replyreviewer --paper <paper.tex> --reviewers <r1.txt> [r2.txt ...] [--title "Title"] [--editor "Name"]

Example:

/replyreviewer --paper sn-article.tex --reviewers .\reviewers\R1.txt .\reviewers\R2.txt --editor "Zhouping Yin"

Argument	Required	Description
`--paper <path.tex>`	Yes	Path to the original LaTeX paper
`--reviewers <files>`	Yes	One `.txt` file per reviewer; first = R1, second = R2, etc.
`--title "..."`	No	Paper title for the letter header; extracted from `\title{}` if omitted
`--editor "..."`	No	Editor name for the salutation; defaults to `[EDITOR NAME]` if omitted

What the agent produces:

One LaTeX response letter per reviewer — <basename>_response_R<N>.tex, each with a formal opening, General Comments, point-by-point Specific Comments, and a Scopus-validated References Added section with clickable DOIs.
Annotated original paper — \added[id=RN]{} / \replaced[id=RN]{}{} / \deleted[id=RN]{} markup, grammar-only fixes applied directly, and \usepackage{changes} with one \definechangesauthor per reviewer (R1 blue, R2 red, R3 orange, R4+ purple) added to the preamble automatically.

Comment categories processed:

Code	Category	Paper change
G	Grammar / spelling	Direct fix, no markup
S	Style / writing	`\replaced[id=RN]{new}{old}`
SC	Scientific issue	`\added[id=RN]{...}`
M	Methodology addition	`\added[id=RN]{...}`
R	Results addition	`\added[id=RN]{...}`
D	Discussion addition	`\added[id=RN]{...}`
FT	Figure / table issue	`\added[id=RN]{...}` new float
EQ	Equation issue	`\replaced[id=RN]{}{}` or `\deleted[id=RN]{}`
REF	Reference suggestion	Scopus-validated, `\added[id=RN]{\cite{}}`
Q	General quality	`\added[id=RN]{...}`
MAJ	Major revision	`\replaced[id=RN]{}{}` / `\deleted[id=RN]{}`

Prerequisites: SCOPUS_API_KEY set; campus network or VPN active.

Related commands: /auditpaper (full audit before/after revision), /bibclean (clean the .bib after adding references), /ref (format individual references).

File: .claude/commands/replyreviewer.md

Agents

Agents are specialists Claude delegates to automatically based on context, or explicitly on request ("use the scopus-auditor agent to…"). Fifteen ship in this repo; most back a slash command. Two of them (local-writer, local-coder) are local-delegation agents: a cheap cloud wrapper that drives a local Ollama model over a Bash bridge (see "Local delegation"). Two are loop orchestrators: authoring-loop (ScholarEval-gated writing loop) and the code loop in the loop-engineer skill (see "Loop engineering").

Format (repo convention): one flat markdown file per agent at .claude/agents/<name>.md, opening with YAML frontmatter (name:, description:). This is what Claude Code's subagent discovery scans; a sub-folder layout is invisible to it. Note the asymmetry with skills, which ARE folder-based (skills/<name>/SKILL.md). The canonical .claude/agents/ files are the single source of truth; per-tool mirrors are generated from them (see "Using the agents outside Claude Code" below).

Agent	Purpose	Command / trigger	Path
`scopus-researcher`	Autonomous literature review: search, validate, summarize, PRISMA + gap/coverage/Pareto matrices, hypotheses, LaTeX output	`/litreview`	`.claude/agents/scopus-researcher.md`
`litreview-updater`	Incrementally refresh an existing review with new papers: windowed Scopus + Consensus search, delta dedup, validation/grading, preemption check (deliberation + scholar-evaluation), dated `\added{}` copy `_up_YYYYMMDD.tex` + CHANGELOG; unattended draft + REVIEW REQUIRED	`/litupdate`	`.claude/agents/litreview-updater.md`
`scopus-auditor`	Audit an existing review; validate every reference; executable improvement plan	`/auditreview`	`.claude/agents/scopus-auditor.md`
`paper-auditor`	Full paper content audit (intro→future works) + Scopus validation + ScholarEval score + improvement plan	`/auditpaper`	`.claude/agents/paper-auditor.md`
`thesis-auditor`	Full UQAC thesis audit (front matter, hypothesis flow, chapter structure, bilingual consistency, UQAC compliance) + ScholarEval score	`/auditthesis`	`.claude/agents/thesis-auditor.md`
`thesis-proposal-auditor`	Audit a UQAC thesis proposal (≤35 pages body, testable hypotheses, suggested methodology, no full results) + ScholarEval score	thesis-proposal audit / by name	`.claude/agents/thesis-proposal-auditor.md`
`reviewer-response`	Point-by-point response letters + traceable `changes`-package markup in the paper	`/replyreviewer`	`.claude/agents/reviewer-response.md`
`bib-cleaner`	Validate, deduplicate, normalize and DOI-enrich a `.bib` file	`/bibclean`	`.claude/agents/bib-cleaner.md`
`submit-checker`	Pass/fail submission checklist against a target journal's requirements	`/submitcheck`	`.claude/agents/submit-checker.md`
`word-to-latex`	Faithful Word `.docx` → LaTeX conversion (pandoc + visual-fidelity patches)	`/word2latex`	`.claude/agents/word-to-latex.md`
`cover-paper`	Submission package: hidden Cover Letter in source, standalone Title Page PDF, Corresponding Author Profile PDF (recent papers from Scopus), Graphical Abstract via Canva MCP from the paper's figures (Elsevier/Springer spec + FigureLabs prompt)	by name (at submission)	`.claude/agents/cover-paper.md`
`thesis-to-paper`	Integrate a thesis + its conference papers into one submission-ready journal manuscript (invited extension); pandoc reference conversion, figure pipeline, content-delta matrix, then `/litreview` + `scientific-writing` + `/bibclean` + `/submitcheck` + `/auditpaper` inline, with a multi-session checkpoint protocol	by name / "extend this paper to a journal version"	`.claude/agents/thesis-to-paper.md`
`authoring-loop`	ScholarEval-gated authoring loop: define subject -> author (Fable 5) -> audit with `scholar-evaluation` (Sonnet/Haiku) -> loop to `min_score` or `max_budget` -> record learnings to memory via `local-writer`. Authoring counterpart of the `loop-engineer` code loop	by name / "improve this to a ScholarEval target under a budget"	`.claude/agents/authoring-loop.md`
`latex-writer`	Bilingual LaTeX authoring: papers (IEEE/Springer/Elsevier), Beamer slides, TiKZ diagrams, thesis	by context (writing)	`.claude/agents/latex-writer.md`
`local-writer`	High-token repetitive writing (docstrings, comments, Markdown docs, Obsidian summaries) via local `ornith:9b` over a Bash bridge; NOT LaTeX text authoring	by context / by name	`.claude/agents/local-writer.md`
`local-coder`	Local code generation against a spec/failing test, refactor snippets, scaffolds via local `qwen3.5:9b` over a Bash bridge; no state-changing git	by context / by name	`.claude/agents/local-coder.md`

The four ScholarEval auditors (scopus-auditor, paper-auditor, thesis-auditor, thesis-proposal-auditor) score the document before writing the plan; after the plan is executed they re-run the scoring on the revised source and report a before/after ScholarEval comparison (baseline vs post), hard-gated so execution only completes when the score improves.

`latex-writer` key rules

TiKZ: relative positioning only (drawio2tikz-converted figures are the sanctioned absolute-coordinate exception); arrows perpendicular; no overlaps
References: peer-reviewed only (IEEE, Springer, Elsevier, Taylor & Francis, Cambridge, Wiley, IET, IOP, ACM, MDPI, ASME, ACME, BioMed Central (BMC)); DOI via hyperref; any other publisher needs user confirmation
Tables: rows = parameters, cols = concepts; bold headers; 10 % grey row shading
Language: French default for UQAC thesis, English for scientific papers
Avoid AI-detectable patterns: zero-width spaces, smart quotes, em dashes, perfect parallel lists

`reviewer-response` key rules

Reviewer files assigned sequentially: first file = R1, second = R2, etc.
Grammar-only fixes (G): applied directly, no markup
Additions \added[id=RN]{}, deletions \deleted[id=RN]{}, rewrites \replaced[id=RN]{}{} (changes package)
Reviewer colors: R1 blue, R2 red, R3 orange, R4+ purple (\definechangesauthor)
Every proposed reference validated via Scopus; [NO DOI] flagged in the summary when applicable

Local delegation (Ollama subagents)

local-writer and local-coder cut cloud cost by keeping the top model as orchestrator and pushing token-heavy generation to local models on the GPU. Each agent runs on a cheap cloud model (Haiku) that only frames the task and drives a local model over a Bash bridge (ollama run ornith:9b for writing, ollama run qwen3.5:9b for code); the bulk text or code is generated locally and free. No gateway is used and cloud stays on your normal subscription auth, so only the small Haiku wrapper spends cloud tokens.

Requirements: Ollama running with the two models pulled (ollama list). Until the 9B models are imported, the bridge falls back to qwen2.5-coder:7b. LiteLLM (~/.litellm/ollama.yaml) is optional and only gives the bridge its keep-alive / context tuning. local-writer never authors LaTeX prose (it may add % comments only); all scientific and LaTeX redaction stays with latex-writer + scientific-writing on the latest cloud Claude model.

Loop engineering (local-model dev loop)

The loop-engineer skill runs a budget-bounded develop-and-improve loop: design → plan → code → comment → test → review → score → correct, repeating until a composite quality gate is met or a hard budget cap is hit. It keeps the best cloud model (Fable 5) as orchestrator/judge, uses cheaper cloud tiers (Opus for plans, Sonnet for execution and review) for the actions, and delegates code and comments to the local local-coder / local-writer agents so the heavy generation is free.

Option contract: --loop --budget <max_usd> --score <min_score> [--max-iters N]. The default stop gate is composite: tests green AND no CRITICAL/HIGH review findings AND aggregate score >= min_score (default 90); a literal 100 is opt-in. The loop also stops on the hard budget cap, the max-iterations cap, or a no-progress plateau. The score aggregates findings from the installed reviewers (/code-review, /security-guidance, pr-review-toolkit, systematic-debugging) plus the betterleaks / pip-audit hooks, with security as a hard floor (any CRITICAL fails the gate regardless of the aggregate). The final merge to a protected branch is human-gated: the loop stops at "ready to merge" and waits for your confirmation. The loop diagram and the use-case diagram are in Architecture.md ("Layer 5 — Loop engineering").

The same loop applies to writing through the authoring-loop agent (the ScholarEval-gated variant): define a subject, author with an authoring agent (/litreview, latex-writer, /replyreviewer, …) on Fable 5, audit with the scholar-evaluation skill on Sonnet or Haiku to get a score, loop until the ScholarEval target or the budget is reached, then record the learnings to memory via local-writer. The five steps are documented in the loop-engineer SKILL.md.

Obsidian knowledge-capture loop

Both loops read and write the Obsidian vault so learnings persist across iterations and projects (Claude Code has no cross-project memory of its own; the vault is that broad memory). local-writer is the single, serialized vault writer; local-coder reads only and hands it any learning. Reads happen at plan time (baked into the plan by brainstorming / writing-plans on the cloud tiers) and, during a run, only by the local agents (task start, checkpoints, error recovery); executing-plans does not read. Writes land in 10_Projets/<projet>/ logs and reusable 30_Ressources/ atomic notes through the ~/bin/obsidian wrapper, with a SessionStart/SessionEnd outbox-flush hook as fallback when Obsidian is closed. Requires Obsidian open with the CLI enabled. Full design in docs/contributor-notes.md section 5; routing in .claude/CLAUDE.md.

Calling an agent explicitly

Agents are normally triggered automatically by context. To invoke one directly, address it by name in your message:

Use the scopus-auditor agent to audit the review in paper_review/literature_review.tex

reviewer-response agent: --paper sn-article.tex --reviewers r1.txt --editor "Prof. Yin"

The slash commands /auditreview, /replyreviewer, /litreview, etc. are thin wrappers that call these agents with the same argument syntax — use the commands for convenience and the explicit agent names when you need finer control or want to chain agents in one message.

Using the agents outside Claude Code

install.ps1 regenerates per-tool mirrors from the canonical .claude/agents/*.md files. Run it after adding or editing an agent, then commit the regenerated output. Add -Personal to also copy the Copilot agent profiles to ~/.copilot/agents/, which makes them available to Copilot CLI in every project (re-run after agent edits to refresh).

Tool	Generated target	Notes
GitHub Copilot (agents)	`.github/agents/<name>.agent.md`	Auto-discovered once on the default branch (GitHub.com agents panel, coding agent, VS Code, Copilot CLI `/agent` or `copilot --agent <name>`). Copilot caps agent prompts at 30,000 characters, so the five large agents ship as stubs that read the canonical file first.
GitHub Copilot (commands)	`.github/prompts/<name>.prompt.md`	One prompt file per task command (13); invoke as `/<name>` in Copilot Chat. The Claude session modes (`concis`, `slim`, `focus`, `ctx`) are skipped.
GitHub Copilot (rules)	`.github/instructions/<name>.instructions.md`	One per `.claude/rules/.md`, applied to all files (`applyTo: "*"`), plus the master `.github/copilot-instructions.md` (mission, agent routing, skills pointer).
GitHub Copilot (skills)	none needed	Skills are plain repo folders (`.claude/skills/<name>/SKILL.md`); Copilot agents read them directly, and the master instructions point there.
OpenCode	`.opencode/agent/<name>.md`	Full body, `description` frontmatter.
Continue	`.continue/rules/researchtools.md`	One rule pointing at the canonical files and routing table.
Aider	`CONVENTIONS.md`	Pointer paragraph (created once, never overwritten).

For global availability in Claude Code (any working directory), install-junctions.ps1 links each .claude/agents/<name>.md into ~/.claude/agents/ per file (symlink; hard-link fallback when Developer Mode is off — re-run after a git pull that changes agents). Skills keep their per-folder junctions.

File Locations Summary

All agents, commands, and skills live under this repository's .claude/ directory.

ResearchTools\
└── .claude\
    ├── agents\                              (16 agents)
    │   ├── scopus-researcher.md       ← /litreview
    │   ├── litreview-updater.md       ← /litupdate
    │   ├── scopus-auditor.md          ← /auditreview
    │   ├── paper-auditor.md           ← /auditpaper
    │   ├── thesis-auditor.md          ← /auditthesis
    │   ├── thesis-proposal-auditor.md ← thesis-proposal audit
    │   ├── reviewer-response.md       ← /replyreviewer
    │   ├── bib-cleaner.md             ← /bibclean
    │   ├── submit-checker.md          ← /submitcheck
    │   ├── word-to-latex.md           ← /word2latex
    │   ├── cover-paper.md             ← submission package
    │   ├── thesis-to-paper.md         ← thesis + conf papers -> journal manuscript
    │   ├── authoring-loop.md          ← ScholarEval-gated authoring loop
    │   ├── latex-writer.md            ← LaTeX authoring
    │   ├── local-writer.md            ← local docs/comments (ornith:9b bridge)
    │   └── local-coder.md             ← local code gen (qwen3.5:9b bridge)
    ├── commands\                            (21 commands)
    │   ├── concis.md   ├── slim.md    ├── focus.md   ├── ctx.md
    │   ├── tikz.md     ├── test.md    ├── doc.md     ├── latex.md
    │   ├── ref.md      ├── litreview.md             ├── litupdate.md
    │   ├── auditreview.md              ├── auditpaper.md
    │   ├── auditthesis.md              ├── bibclean.md
    │   ├── submitcheck.md              ├── replyreviewer.md
    │   ├── word2latex.md               ├── geolocalisation.md
    │   ├── loopdev.md
    │   └── recommendation-letter.md
    ├── rules\                               (code-style, preferences, security, testing, workflows)
    └── skills\                              (11 skills)
        ├── scopus\
        │   ├── SKILL.md
        │   └── scripts\  (scopus_api.py, semantic_scholar_api.py, download_pdf.py,
        │                  bib_batch.py, litreview_update.py,
        │                  gemini_reviewer.py, github_reviewer.py, gemini_table.py)
        ├── scientific-writing\SKILL.md
        ├── scholar-evaluation\SKILL.md      (+ scripts\calculate_scores.py)
        ├── deliberation\SKILL.md            (+ scripts\deliberate.py)
        ├── extract-statistic\SKILL.md       (+ scripts\extract_text.py [--stats-scan / --section-scan];
        │                  references\statistical-audit-protocol.md, domain-profiles.md)
        ├── extract-futureworks\SKILL.md     (no script; reuses extract_text.py --section-scan;
        │                  references\futureworks-protocol.md, section-cues.md)
        ├── word2latex\SKILL.md              (+ scripts\docx_inspect.py, manuscript_bib.py)
        ├── drawio2tikz\SKILL.md             (+ scripts\drawio2tikz.py;
        │                  references\conversion-rules.md)
        ├── geolocalisation\SKILL.md         (+ scripts\extract_locations.py, generate_geomap.py,
        │                  Test\test_extract_locations.py; references\geocoding-protocol.md;
        │                  data\ Natural Earth gazetteer cache)
        ├── loop-engineer\SKILL.md           (+ scripts\loop_engineer.py [Agent SDK driver],
                           loop_audit.py [code-quality scorer], Test\test_loop_audit.py;
                           references\ LOOP/STATE/PROCESS/ledger templates; requirements.txt)
        └── recommendation-letter\SKILL.md   (+ scripts\generate_letter.py, letter_templates.py,
                           Test\test_generate_letter.py; references\quality-patterns.md; evals\)

Name		Name	Last commit message	Last commit date
Latest commit History 66 Commits
.claude		.claude
.continue/rules		.continue/rules
.github		.github
.opencode/agent		.opencode/agent
.vscode		.vscode
docs		docs
profiles		profiles
.gitignore		.gitignore
Architecture.md		Architecture.md
CLAUDE (up).md		CLAUDE (up).md
CLAUDE.template.md		CLAUDE.template.md
CONVENTIONS.md		CONVENTIONS.md
LICENSE		LICENSE
NEW_ARCHITECTURE.md		NEW_ARCHITECTURE.md
README.md		README.md
ResearchToolsLogo.png		ResearchToolsLogo.png
install-junctions.ps1		install-junctions.ps1
install.ps1		install.ps1
setup.ps1		setup.ps1

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ResearchTools — Manual

Purpose

TODO in 2026

About this manual

Installation

Install scripts overview

Prerequisites

Step 1 — Clone the repository

Step 2 — Generate machine-local configuration

Step 3 — Make agents available globally (optional, recommended)

Step 4 — Install for other coding tools (optional)

Contributing improvements

Profiles

Environment variables / API keys

Token Management

Output modes

Recommended workflow

Quick reference

Skills

/scopus — Scopus academic search

geolocalisation — corpus study-location mapping

recommendation-letter — support / recommendation / acceptance / dispense letters

Security audit (SkillSpector)

Commands (Slash Commands)

/concis — Concise mode

/focus <topic> — Session scope

/ctx — Context window audit

/tikz — TiKZ validation

/test [module] — Run project tests

/doc <target> — Documentation generator

/latex — LaTeX diagnosis and fix

/ref <citation> — Academic reference formatter

/replyreviewer — Peer reviewer response generator

Agents

latex-writer key rules

reviewer-response key rules

Local delegation (Ollama subagents)

Loop engineering (local-model dev loop)

Obsidian knowledge-capture loop

Calling an agent explicitly

Using the agents outside Claude Code

File Locations Summary

About

Resources

Stars

Watchers

Forks

Releases

Packages

Contributors

Languages

`/scopus` — Scopus academic search

`geolocalisation` — corpus study-location mapping

`/concis` — Concise mode

`/focus <topic>` — Session scope

`/ctx` — Context window audit

`/tikz` — TiKZ validation

`/test [module]` — Run project tests

`/doc <target>` — Documentation generator

`/latex` — LaTeX diagnosis and fix

`/ref <citation>` — Academic reference formatter

`/replyreviewer` — Peer reviewer response generator

`latex-writer` key rules

`reviewer-response` key rules