flonat/claude-research

audit-project-research

Use when you need to audit a research project against the init-project-research template.

bib-validate

Use when you need to validate a paper's bibliography — cross-references \cite{} keys against .bib files or embedded \bibitem entries, finds missing/unused/typo'd keys, and checks every key against the Paperpile library via the local resolver. Deep…

init-project-research

Use when you need to bootstrap a full research project with directory scaffold and Overleaf symlink.

preprint

Use when you need to create a preprint / working-paper variant of a paper currently in conference or journal format. Forks the existing Overleaf project — adds a `preprint/` subfolder using the user's `your-template` Template, ports the body content from the…

proofread

Use when you need academic proofreading of a LaTeX paper (11 check categories).

replication-package

Use when you need to assemble, anonymize, or audit a replication package.

review-cluster

Use when you need a mid-draft adversarial review of a paper — runs paper-critic + domain-reviewer + claim-verify + blindspot in parallel, then auto-synthesises into a prioritised revision plan. Distinct from /pre-submission-report (final-gate kitchen sink, 13…

tailscale-mosh-recover

Use when mosh hangs / fails to connect to a headless Mac mini after a Tailscale update or restart, OR when a remote-access tool (RustDesk, VNC, AnyDesk) fails to reach its public relay from an MDM-managed client. Layers — Tailscale daemon health (dual-install…

wiki-grow

Use when you want to auto-promote project knowledge articles into vault wiki concepts. Saturday cron job — runs the corpus scanner, picks candidates above threshold, copies each source article into ~/vault/concepts/ with auto_generated frontmatter so it…

init-paper-book

Use when you need to scaffold a NEW educational companion book for a LaTeX paper. Reads the paper, drafts 8 substantive chapters into the vault at ~/vault/books/{slug}/, copies bib + figures, registers the book, and verifies atlas serves it. Source-of-truth…

audit-paper-book

Use when you need to detect drift between an existing paper-book companion and a revised version of its source paper, then sync the mechanical pieces (new bib entries, new/changed figures) and report the substantive drift (renamed sections, changed numbers,…

bib-parse

Use when you need to extract citations from a PDF and generate a validated .bib file. Reads the PDF, identifies all referenced works, constructs BibTeX entries with metadata verification, then runs /bib-validate.

checkpoint

Use when you need to save session state to survive context compaction or handoff between sessions.

compile-knowledge

Use when you need to compile raw inputs (literature, meeting notes, session logs, code findings) into a per-project knowledge wiki. Supports --autonomous / -y for end-to-end runs without prompts (used by the Saturday wiki-grow cron).

gather-readings

Use when you need to gather PDFs from Paperpile into a project's articles/ folder.

grill-me

Use when you want to be interrogated ONE question at a time — either to (a) defend your own research (viva, job talk, seminar Q&A, hostile-referee prep) or (b) study a class / subject you're learning (exam revision, active recall). An interactive…

ideas

Use when you need to capture or integrate improvement ideas for Claude Code infrastructure.

knowledge-lint

Use when you need to check compiled knowledge for contradictions, uncited claims, missing connections, stale articles, and orphaned concepts.

lean-check

Use when you need to MACHINE-CHECK a self-authored lemma/theorem by formalizing it in Lean 4 + mathlib and running `lake build` — the strongest verification (a clean build with no `sorry` IS a proof). R3 of the verification spectrum. Runs against the…

literature

Use when you need academic literature discovery, synthesis, or bibliography management. Supports standalone searches and end-to-end project pipelines with vault sync and auto-commit.

minutes-cleanup

Manage old recordings — find large files, archive old meetings, delete processed originals. Use when the user says "clean up recordings", "how much space are meetings using", "delete old recordings", "archive meetings", "manage meeting storage", or asks about…

minutes-debrief

Post-meeting debrief — analyzes what happened, compares outcomes to your prep intentions, tracks decision evolution. Use when the user says "debrief", "what just happened in that meeting", "what did we decide", "debrief that call", "post-meeting", "what…

minutes-list

List recent meetings and voice memos. Use when the user asks "what meetings did I have", "show my recent recordings", "any meetings today", "list my voice memos", or wants an overview of their meeting history. Also use when they need to find a specific…

minutes-prep

Interactive meeting preparation — builds a relationship brief and talking points before a call. Use when the user says "prep me for my call with", "I'm meeting with X", "prepare me for", "what should I bring up with", "meeting prep", "get ready for my call",…

minutes-recap

Generate a daily digest of today's meetings and voice memos — key decisions, action items, and themes across all recordings. Use when the user asks "recap my day", "what happened in my meetings today", "daily summary", "what did I discuss today", "any action…

minutes-search

Search past meeting transcripts and voice memos for specific topics, people, decisions, or ideas. Use this whenever the user asks "what did we discuss about X", "find that meeting where we talked about Y", "what did Alex say", "did we decide on", "what was…

minutes-verify

Verify that the meeting-transcribe pipeline is properly set up — whisper/ffmpeg/uv binaries, models, package venv, watcher, and folders. Use when the user says "is transcription working", "check my meeting setup", "verify minutes", "why isn't transcription…

minutes-weekly

Weekly meeting synthesis — themes, decision arcs, stale commitments, and what deserves your attention next week. Use when the user says "weekly review", "what happened this week", "weekly summary", "recap my week", "any outstanding items", "week in review",…

preregister

Use when the user needs to write a preregistration for an empirical study before collecting data — OSF-Standard 'Pre-Data Collection Registration' by default, or the shorter AsPredicted 9-question form via `--aspredicted`. Triggers on phrases like…

rename-project-research

Use when you need to rename a research project across all systems (local directory, atlas, vault, Overleaf, git).

reorg

Use when you need content-aware file reorganisation or deduplication driven by a LOCAL model (Ollama on the Mac Mini) that actually reads each file's contents, not just its name — proposes a folder structure or finds exact/near duplicates, always dry-runs…

retarget-journal

Use when you need to retarget a paper to a different journal (rename, swap bib, update citations).

session-close

Use when you need to run the end-of-session checklist (uncommitted changes, focus update, project sync). Auto-detects research projects and adds atlas consistency checks.

skill-health

Use when you need a dashboard of skill invocation counts, success rates, failure patterns, and health status. Reads JSONL logs and qualitative observations. Reporting only — never auto-modifies skills.

sync-permissions

Use when you need to sync global permissions into the current project.

task-management

Use when you need help with daily planning, weekly reviews, meeting actions, or vault task queries.

wiki-curate

Use when you need to audit the vault wiki (~/vault/concepts/) for fragmentation, missing tags, write-only concepts, and draft/anatomy conformance. Read-only — produces a markdown report at /tmp/wiki-curate-report.md. Companion to /wiki-grow (which writes) and…

wiki-merge

Use when /wiki-curate has identified an overlap cluster and you want to collapse it. Takes a canonical winner slug + one or more fold-in slugs; merges bodies, rewrites all [[wikilink]] references in the corpus, deletes losers, denylists them. Dry-run by…

wire-shared-package

Use when you need to wire a shared Python package as an editable dependency across projects.

brief-compliance-check

Use when you need to check a LaTeX submission against a PDF assessment brief.