Sage-Bionetworks

Compact the current conversation into a handoff document for another agent to pick up.

Reference guide for implementing and configuring Comparison Tool (CT) repository classes that extend ComparisonToolRepositorySupport. Use this skill whenever the user is: creating a new CT repository, adding a sort column to an existing CT, debugging unexpected sort order (null rows floating up, wrong column ordering), configuring filters or search for a CT, reviewing a CT repository implementation, or asking how to wire up any part of the CT backend pipeline (sort hooks, filter config, base criteria, spaced field names, heatmap columns, array columns, computed/fallback fields). Trigger phrases include "new CT", "comparison tool", "CT repository", "CT sort", "null rows", "empty rows", "sort order", "heatmap column sort", "array column sort", "getComputedSortFieldExpressions", "getSortFieldAliases", "ComparisonToolRepositorySupport", "CtFilterConfig".

Generates a PR title and description body following repository template standards. Use this skill whenever the user asks to create, write, generate, or update a PR description, or when working with an active pull request that needs documentation. Also use this when the user says things like "write up this PR", "draft the PR", "prepare the PR", or "describe these changes".

Evaluates a proposed version bump for a GitHub Action, reusable workflow, or composite action by comparing the upstream changelog against how the action is actually used in this repo. Use this skill whenever the user mentions bumping, upgrading, updating, or evaluating a version change for anything referenced via `uses:` in `.github/workflows/` *or* `.github/actions/` -- including phrases like "should we upgrade X", "is it safe to bump Y from A to B", "evaluate breaking changes for Z", "Dependabot opened a PR for...", or "what changes between v4 and v7 of...". Trigger even when the user doesn't explicitly say "evaluate" -- if they're asking about the impact of a workflow dependency version change, run this.

Generates monthly update pages for the Sage monorepo documentation site, aggregating all pull requests merged to `main` during a given month into a structured, user-friendly page. Use this skill whenever someone asks for a monthly update, monthly summary, monthly changelog, or wants to create/regenerate the docs page for a specific month — even if they just say "generate the update for March" or "add April to the docs". Trigger on phrases like "monthly update", "monthly summary", "create the update for [month]", "add [month] to the docs", or "regenerate [month-year].md".

Generates standardized weekly updates for the Sage-Bionetworks/sage-monorepo project, summarizing merged PRs, contributor activity, and project progress. Use this skill whenever someone asks for a weekly update, weekly summary, digest of merged PRs, progress report, standup notes, or anything that sounds like a periodic status update for stakeholders — even if they don't explicitly say "weekly update". Trigger on phrases like "what got done this week", "summarize the PRs", "create our weekly digest", "weekly standup summary", or "what did the team ship".

Systematically patches security vulnerabilities in this pnpm monorepo. Use this skill whenever the user wants to fix CVEs, address pnpm audit findings, update vulnerable dependencies, or patch security vulnerabilities. Trigger on phrases like "fix vulnerabilities", "patch CVEs", "address security audit", "update vulnerable deps", "investigate <package> dependency", or any mention of pnpm audit results or GHSA advisories.

Write unit tests for one or more files following this codebase's conventions (Vitest, Testing Library, inline mocks). Use this skill whenever the user asks to write, add, or generate tests — including "write tests for X", "add test coverage", "test this component", or "how do I test this".

Answer questions about SWC ↔ SRC integration — connecting the GWT-based Synapse Web Client (SWC) with React components from synapse-react-client (SRC). Use this skill whenever the user asks about JsInterop, rendering React components in GWT views, prop classes for SRC components, Synapse context across applications, or any SWC/SRC interoperability topic. Trigger even if the user just mentions "SWC", "GWT", or asks why a React component isn't rendering in SWC.

Create initial CLAUDE.md files for a repo with none — auto-detects stack, pulls context from GitHub/Jira/Confluence, produces concise files focused on non-obvious patterns.

Update existing CLAUDE.md files by analyzing code changes, GitHub PRs/issues, Jira/Confluence since last modification, with full accuracy audit.

Query the NIH RePORTER API (api.reporter.nih.gov) for federally-funded research projects and publications. Covers POST /v2/projects/search and POST /v2/publications/search — criteria payload construction, pagination, rate-limit handling, and the criteria→response field-name mapping that trips up most callers.

Systematically patches security vulnerabilities in pnpm projects. Use this skill whenever the user wants to fix CVEs, address pnpm audit findings, update vulnerable dependencies, or patch security vulnerabilities. Trigger on phrases like "fix vulnerabilities", "patch CVEs", "address security audit", "update vulnerable deps", "investigate <package> dependency", or any mention of pnpm audit results or GHSA advisories.