retarget-journal

3

flonat

Retarget a paper to a different journal. Renames folders, swaps bib files, updates citation keys, reformats to target requirements, and compiles to verify.

insights-deck

3

flonat

Generate timestamped Claude Code insights report and Beamer presentation. Runs /insights, archives HTML, then builds a rhetoric-driven deck from the findings.

init-project

3

flonat

Bootstrap a new research project. Interview for details, scaffold directory structure, create an Overleaf symlink, initialize git, and create project context files.

quarto-deck

3

flonat

Generate Reveal.js HTML presentations from Markdown. Applies rhetoric principles (assertion titles, one idea per slide, narrative arc). Best for teaching, informal talks, and web-shareable decks.

project-safety

3

flonat

Set up safety rules and folder structures for research projects. Prevent accidental data loss when Claude reorganizes files.

insights-deck

3

flonat

Generate timestamped Claude Code insights report and Beamer presentation. Runs /insights, archives HTML, then builds a rhetoric-driven deck from the findings.

Project Deck

3

flonat

Create presentation decks to communicate project status. For supervisor meetings, coauthor handoffs, or documenting progress.

system-audit

3

flonat

Run parallel system audits across skills, hooks, agents, rules, bibliographies, conventions, and documentation freshness. Report-only — never modifies files.

pipeline-manifest

3

flonat

Build a pipeline manifest mapping scripts to inputs, outputs, and paper figures/tables. Optionally add structured headers to scripts.

lessons-learned

3

flonat

Structured, blameless post-mortem process for incidents, mistakes, or stalled sessions. Converts problems into systematic improvements (skills, guards, docs, hooks). Use when something went wrong or when stakeholders ask 'how do we prevent this?'.

code-archaeology

3

flonat

Systematically review and understand old code, data, and analysis files. For reviving old projects, auditing inherited code, or preparing for R&R.

pre-submission-report

3

flonat

Run all quality checks and produce a single dated report before submission or sharing.

sync-notion

3

flonat

Sync the current project's state to the central context library and Notion. Updates projects/_index.md, current-focus.md, and the Research Pipeline database entry.

Project Deck

3

flonat

Create presentation decks to communicate project status. For supervisor meetings, coauthor handoffs, or documenting progress.

update-project-doc

3

flonat

Update a project's own documentation (CLAUDE.md, README.md, docs/*.md) to reflect its current state. Detects stale file trees, timestamps, counts, and next steps.

quarto-deck

3

flonat

Generate Reveal.js HTML presentations from Markdown. Applies rhetoric principles (assertion titles, one idea per slide, narrative arc). Best for teaching, informal talks, and web-shareable decks.

beamer-deck

3

flonat

Generate academic Beamer presentations with multi-agent review. Builds original themes, applies rhetoric principles, iterates until zero warnings.

Project Safety

3

flonat

Set up safety rules and folder structures for research projects. Prevent accidental data loss when Claude reorganizes files.

python-env

3

flonat

Python environment management with uv. ALWAYS use uv for package management, never pip directly. Triggers: "install package", "create venv", "set up Python". Not for running scripts — just use `uv run python`.

creation-guard

3

flonat

Pre-flight duplicate check before creating new skills or agents. Prevents duplicates and suggests iterations. MUST be invoked before writing any new artifact definition.

process-reviews

3

flonat

Process referee comments from a reviews PDF into standardised tracking files: comment tracker, review analysis, and LaTeX verbatim transcription.

latex

3

flonat

LaTeX document compilation and management. When Claude needs to compile LaTeX documents (.tex files) for papers, presentations, or other academic content.

literature

3

flonat

Academic literature discovery, synthesis, and bibliography management. Find papers, verify citations, create .bib files, download PDFs, and synthesize literature narratives. Includes OpenAlex API integration for structured scholarly queries.

insights-deck

3

flonat

Generate timestamped Claude Code insights report and Beamer presentation. Runs /insights, archives HTML, then builds a rhetoric-driven deck from the findings.

literature

3

flonat

Academic literature discovery, synthesis, and bibliography management. Find papers, verify citations, create .bib files, download PDFs, and synthesize literature narratives. Includes OpenAlex, Scopus, and Web of Science API integration for structured scholarly queries.

pipeline-manifest

3

flonat

Build a pipeline manifest mapping scripts to inputs, outputs, and paper figures/tables. Optionally add structured headers to scripts.

Project Safety

3

flonat

Set up safety rules and folder structures for research projects. Prevent accidental data loss when Claude reorganizes files.

Multi-Perspective

3

flonat

Explore a research question from multiple independent perspectives with diverse epistemic priors. Spawns parallel agents with distinct disciplinary lenses, then synthesises findings.

update-focus

3

flonat

Update current-focus.md with a structured session summary. Preserves the document's rich structure: weekly focus, session history rotation, open loops, mental state. Use at end of work sessions or when the stop hook nudges.

system-audit

3

flonat

Run parallel system audits across skills, hooks, agents, rules, bibliographies, conventions, and documentation freshness. Report-only — never modifies files.

update-project-doc

3

flonat

Update a project's own documentation (CLAUDE.md, README.md, docs/*.md) to reflect its current state. Detects stale file trees, timestamps, counts, and next steps. Includes a leanness audit: flags CLAUDE.md > 200 lines, sections > 15 lines of reference material, and SKILL.md > 300 lines — with auto-extraction to docs/ or references/.

interview-me

3

flonat

Interactive interview to formalise a research idea into a structured specification with hypotheses and empirical strategy. Conversational — asks questions one at a time. Triggers: 'help me formalise this idea', 'develop my research question'. Not for literature search — use /literature.

save-context

3

flonat

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humanizer

3

flonat

Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's comprehensive "Signs of AI writing" guide. Detects and fixes patterns including: inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases.

latex-autofix

3

flonat

LaTeX compilation with autonomous error resolution. Build artifacts go to out/, PDF is copied back to source directory. Parses logs, auto-fixes known errors (missing packages, font conflicts, citation issues, bad paths, stale cache), and runs citation audit on success.

session-recap

3

flonat

End-of-session checklist. Checks for uncommitted changes, offers to update focus, project docs, context, and session log. Replaces the old stop hook.

init-project

3

flonat

Bootstrap a new research project. Interview for details, scaffold directory structure, create Overleaf symlink, initialise git, and create project context files.

update-project-doc

3

flonat

Update a project's own documentation (CLAUDE.md, README.md, docs/*.md) to reflect its current state. Detects stale file trees, timestamps, counts, and next steps.

learn

3

flonat

Extract reusable knowledge from the current session into a persistent skill. Use when you discover something non-obvious, create a workaround, or develop a multi-step workflow that future sessions would benefit from.

research-ideation

3

flonat

Generate structured research questions, testable hypotheses, and empirical strategies from a topic or dataset. Produces 3–5 ranked questions with identification strategies.

code-archaeology

3

flonat

Systematically review and understand old code, data, and analysis files. For reviving old projects, auditing inherited code, or preparing for R&R.

validate-bib

3

flonat

Cross-reference \cite{} keys against .bib files or embedded \bibitem entries. Finds missing, unused, and typo'd citation keys. Deep verification mode spawns parallel agents for DOI/metadata validation at scale. Read-only in standard mode.

validate-bib

3

flonat

Cross-reference \cite{} keys against .bib files or embedded \bibitem entries. Finds missing, unused, and typo'd citation keys. Read-only — never edits files.

learn

3

flonat

Extract reusable knowledge from the current session into a persistent skill. Use when you discover something non-obvious, create a workaround, or develop a multi-step workflow that future sessions would benefit from.

system-audit

3

flonat

Run parallel system audits across skills, hooks, agents, rules, bibliographies, conventions, and documentation freshness. Report-only — never modifies files.

LaTeX

3

flonat

LaTeX document compilation and management. Use when Claude needs to compile LaTeX documents (.tex files) for papers, presentations, or other academic content.

pipeline-manifest

3

flonat

Build a pipeline manifest mapping scripts to inputs, outputs, and paper figures/tables. Optionally add structured headers to scripts.

LaTeX

3

flonat

LaTeX document compilation and management. When Claude needs to compile LaTeX documents (.tex files) for papers, presentations, or other academic content.