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
Automate browser interactions and inspect or test web pages through Playwright commands. Use when the task requires deterministic browser navigation, screenshots, selectors, or Playwright-test work. For a full local-webapp test workflow, use $webapp-testing.
Command Claude Code
Deliver a structured post-mortem after incidents, mistakes, or stuck sessions. Use when the user requests a structured post-mortem after incidents, mistakes, or stuck sessions.
Command Claude Code
Deliver a fast pre-commit safety scan: file size, anonymity (author / affiliation strings in tex/bib), hardcoded secrets, and invisible-Unicode carriers. Use when the user requests a fast pre-commit safety scan: file size, anonymity (author / affiliation strings in tex/bib), hardcoded secrets, and invisible-Unicode…
Command Claude Code
Run the final, comprehensive submission-readiness gate and consolidate all checks into one dated report; citation-integrity-only mode is also supported. Use when a paper and submission package are nearly final. Not for a mid-draft adversarial review; use $review-cluster.
Command Claude Code
Create a concise presentation deck that communicates a project's current state, decisions, evidence, risks, and next steps. Use when preparing a project update for collaborators, supervisors, or stakeholders. Not for a research talk centered on one paper; use $talk-deck.
Command Claude Code
Install or reconcile research-project safety rules and protected folder boundaries for data, code, outputs, and paper sources. Use when a project lacks guardrails or is being migrated into the governed structure. Not for auditing the full research scaffold; use $audit-project-research.
Command Claude Code
Improve the exposition and readability of a mathematical proof already verified as correct without changing its mathematics. Use when polishing a lemma, theorem, proof, or appendix after correctness checks. Not for verifying the proof; use $verify-math.
Command Claude Code
Proofread a LaTeX academic paper across eleven language, notation, citation, and consistency categories. Use when the requested task is bounded proofreading rather than substantive rewriting, clarity stress-testing, or venue compliance.
Command Claude Code
Create and maintain Python environments and dependencies with uv. Use when installing packages, creating a virtual environment, resolving Python dependency state, or migrating away from pip. Not for general Python coding.
Command Claude Code
Generate a Reveal.js HTML presentation from Markdown. Use when the user asks to generate a Reveal.js HTML presentation from Markdown.
Command Claude Code
Propose and, after approval, execute content-aware file reorganization or deduplication using a local Mac Mini model with a reversible undo record. Use when sorting a folder by file contents or finding exact and near duplicates. Always dry-runs first.
Command Claude Code
Map claims in a literature to independent replications, robustness checks, failures, and unresolved evidence gaps. Use when assessing the empirical reliability of a body of findings rather than reproducing one project's code. For package rerunnability, use $replication-package.
Command Claude Code
Assemble, anonymize, validate, or audit a research replication package. Use when preparing code and permitted data for reviewer or public release. Not for auditing code quality alone; use $code-suite or $replication-audit as appropriate.
Command Claude Code
Retarget an active manuscript to a different journal by reconciling venue identity, files, bibliography, citations, and submission-facing metadata. Use when a new target journal has already been chosen and the paper package must change. Not for choosing a venue; use the venue-fit workflow.
Command Claude Code
Deliver a mid-draft adversarial review of a paper — runs paper-critic + domain-reviewer + claim-verify + blindspot in parallel, optionally adds clarity-reviewer, then auto-synthesises into a prioritised revision plan. Use when the user requests a mid-draft adversarial review of a paper — runs paper-critic +…
Command Claude Code
Systematic reviewer response workflow: parse comments, classify by severity, develop response strategy, write structured rebuttal. Use when asked to 'write rebuttal', 'respond to reviewers', 'draft review response', or 'handle R&R'.
Command Claude Code
Check whether the current session has coherent guidance, focus, handoff state, working-tree ownership, and enough context to proceed safely. Use when starting, resuming, or diagnosing a confused session. Not for auditing the machine or deployed AI infrastructure; use $system-audit.
Command Claude Code
Create a timestamped research-session progress log that records completed work, evidence, decisions, and next steps. Use when closing or checkpointing substantive project work that needs a durable chronology. Not for saving one reusable finding; use $store-insight.
Command Claude Code
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.
Command Claude Code
Deliver a pre-flight duplicate check before creating new skills or agents. Use when the user requests a pre-flight duplicate check before creating new skills or agents.
Command Claude Code
Download, split, and deeply read an academic PDF that is not available through Paperpile. Use when a long external PDF needs page-wise ingestion. For Paperpile items, use the Paperpile text-extraction route instead.
Command Claude Code
Turn external referee correspondence or internal pre-submission feedback into a provenance-safe, DAG-validated revision master plan with atomic tasks, dependencies, critical path, and execution blocks. Use when feedback exists but must be converted into an approved implementation sequence. Not for drafting the…
Command Claude Code
Use SymPy to prove or refute a self-authored algebraic identity, derivative, limit, comparative-static sign, or closed form. Use when exact symbolic manipulation can settle the claim. For parameter sweeps or full theorem proving, use $numerical-check or $lean-check.
Command Claude Code
Deduplicate and reconcile multiple completed review reports into one prioritised revision plan with conflicts and dependencies made explicit. Use when parallel reviewers have returned findings that need a single action sequence. Not for running the reviews; use $review-cluster.
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: