Shareable Claude Code + Codex infrastructure for PhD researchers — skills, agents, hooks, and rules for academic workflows
This repository also configures its own agents. See what flonat-research tells them →
Command Claude Code
Generate structurally realistic synthetic datasets for pipeline prototyping, test coverage, or prospective power analysis. Use when code or design must be exercised before real data are available or accessible. Never substitute synthetic records for governed raw data.
Command Claude Code
Diagnose and recover Mac Mini remote-access failures across Tailscale, mosh, resolver state, and public relays. Use when mosh hangs, the headless Mini disappears after a Tailscale change, or RustDesk/VNC/AnyDesk cannot reach its relay. Not for ordinary machine synchronization.
Command Claude Code
Query and update recorded planning and research portfolio state across tasks, topics, papers, outputs, submissions, venues, people, institutions, and deadlines. Use when asking what is already recorded, including institution- or venue-associated topics, or when doing daily planning and weekly review. For venue…
Command Claude Code
Autonomously diagnose a codebase, apply minimal fixes, and rerun tests until they pass or a real blocker is reached. Use when the user explicitly requests an iterative fix-until-green loop across Python, R, Julia, or HPC workflows.
Command Claude Code
Diagnose and fix residual TikZ label, arrow, box, and Bézier-path collisions with geometric calculations. Use when a generated .tex figure has overlapping labels or crossed arrows. Not for generating a new figure; use $figure or the upstream deck workflow.
Command Claude Code
Update current-focus.md with a structured session summary. Use when the user asks to update current-focus.md with a structured session summary.
Command Claude Code
Update a project's own CLAUDE.md, README.md, or docs/ to reflect current state. Use when the user asks to update a project's own CLAUDE.md, README.md, or docs/ to reflect current state.
Command Claude Code
Fork an existing paper into a concurrent second-venue submission variant with policy checks, separate Overleaf ownership, format conversion, budget refit, QA, and Atlas/Vault writeback. Use when submitting the same work concurrently to another permitted venue. Not for preprints, ordinary retargeting, or camera-ready…
Command Claude Code
Audit a paper and submission package against current official venue requirements for its venue, track, article type, cycle, and stage. Use when checking templates, limits, anonymity, declarations, or required files before submission or inside $pre-submission-report. Not for venue recommendations.
Command Claude Code
Verify a self-authored mathematical result end to end by routing claims across adversarial review, numerical falsification, symbolic or CAS checks, and Lean, then aggregating one report. Use when a theorem, proposition, conjecture, or paper-wide mathematical argument needs the appropriate combination of verification…
Command Claude Code
Analyze representative writing samples into a portable personal voice profile and style guide. Use when establishing voice-matched editing for a new project or refreshing an outdated profile. Not for a target journal's editorial style; use $journal-voice.
Command Claude Code
Edit draft or auto-generated prose to match an existing personal voice profile. Use when transforming generic text into the profiled author's wording, cadence, and style. Not for creating the profile or matching a journal; use $voice-analyzer or $journal-voice.
Command Claude Code
Identify recurring weak arguments, unsupported assumptions, and vulnerable inference patterns across a literature corpus. Use when stress-testing a body of work rather than reviewing one manuscript. For one paper's argument, use the appropriate paper-review workflow.
Command Claude Code
Exercise and verify a local web application through Playwright, including user flows and rendered behaviour. Use when testing a running local app rather than issuing an isolated browser command. For ad hoc automation, use $playwright-cli.
Command Claude Code
Audit the Research Vault concept wiki read-only for fragmentation, missing tags, write-only concepts, and draft or anatomy conformance, producing a Markdown report. Use when assessing wiki quality before maintenance. Not for promoting or merging concepts; use $wiki-grow or $wiki-merge.
Command Claude Code
Auto-promote eligible project knowledge articles into Research Vault concepts with generated provenance metadata. Use when running the scheduled knowledge-corpus promotion or previewing candidates interactively. Not for consolidating overlapping concepts; use $wiki-merge.
Command Claude Code
Merge an overlap cluster of Vault concepts into one canonical concept, rewrite wikilinks, and preserve a dry-run/apply boundary. Use when $wiki-curate has identified a winner and fold-in slugs. Not for general wiki auditing or automatic article promotion.
Command Claude Code
Add or repair an editable shared Python-package dependency across consuming projects, including clone-local configuration and verification. Use when multiple repositories must import the same local package source. Not for one project's ordinary environment setup; use $python-env.
Command Claude Code
Create, read, edit, clean, format, chart, or convert spreadsheet files while preserving spreadsheet-native deliverables. Use when .xlsx, .xlsm, .csv, or .tsv data is the primary input or a spreadsheet is the requested output. Not for Word documents, HTML reports, standalone scripts, database pipelines, or Google…
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: