Comments
Code comments and annotations
autoship
by bdfinst
Orchestrate a bounded round of automated issue processing: reclaim orphaned in-progress issues, discover eligible autoship:ready issues, and invoke /ship sequentially for each — stopping at cost or count caps and surfacing blocked items without halting the round. Requires --max-issues and --max-cost-usd. Use when you want a self-contained automated delivery round driven from the issue tracker.
semantic-duplication-scan
by bdfinst
Detect business logic reimplemented in multiple architectural layers. Builds a persistent computation-register.json by annotating non-trivial computation functions with structured semantic descriptions, then clusters entries to surface duplicate domain concepts. Runs in full-scan mode on first use, incremental (git-diff-based) mode on subsequent runs. Use when the user wants to find logical duplication that linters and diff-scoped review agents miss — the same domain calculation independently reimplemented across layers.
gherkin-derive
by bdfinst
Derive Gherkin scenarios directly from a codebase — standalone, with no prior legacy-modernization analysis. Discovers the public surface (OpenAPI, routes, existing tests, exported signatures, plus message-queue, cron, and websocket/GraphQL surfaces), recommends a BDD binding mode via the bdd-value-guide rubric, and merges scenarios into .feature files (preserving prior enrichment, never overwriting) plus (in bdd-runner mode) pending step-definition stubs. Use it on its own to capture intended behavior before changing tests, or as Phase 3 of /test-improve. Creates no tracker Stories.
last-30-days-research
by mohitagw15856
"Searches Reddit, X/Twitter, and the broader web for recent opinions, sentiment, and signal on any topic. Use when you need to know what real people are saying about a tool, product, trend, or event in the past 30 days — cutting through SEO content to surface genuine community reaction. Produces a structured report with consensus findings, pain points, positive signals, contrarian takes, source links, and a signal confidence rating."
Agentspan — Build Durable AI Agents
by agentspan-ai
Claude Code tools are strings — ["Read", "Edit", "Bash"], not @tool functions
clinvar-database
by jimmc414
"Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine."
local-review
by windmill-labs
Code review the current PR (or branch diff against main) for bugs, security, and AGENTS.md compliance. MUST use when asked to review code.
pr
by windmill-labs
Open a draft pull request on GitHub and drive CI review rounds until it is ready. MUST use when you want to create/open a PR.
write-flow
by windmill-labs
MUST use when creating flows.
uipath-rules
by UiPath
"UiPath Business Rules — .dmn decision tables (DMN 1.5, FEEL) in a BusinessRules project (project.uiproj), built with uip rules (init, refresh, validate, debug). Author, edit, review, validate, and debug a rule's decision table from a policy, spreadsheet, or description; list and describe deployed rules. For .bpmn business rule tasks->uipath-maestro-bpmn. For EvaluateBusinessRule in .xaml->uipath-rpa. For caseplan.json business rule tasks->uipath-maestro-case. For solution pack/publish/deploy->uipath-solution."
uipath-knowledge-bundles
by UiPath
"Read and publish UiPath knowledge bundles via uip or kb — versioned sets of markdown documents (Open Knowledge Format) that live in an Orchestrator folder and that an agent reads from as context. Download a version into a local workspace, read one file or a whole version, publish a directory as version 1, and ask what a local copy needs to match a published version. PREVIEW: these commands exist only on a prerelease uip build and only on tenants with the knowledge-bundles feature enabled — Step 0 below is how you find out, and a miss means stopping, not improvising. Changing published content goes through a reviewed change proposal: uip or kb change-proposal opens one from an edited workspace, carries the review comments, and merges it to publish the next version. For Orchestrator assets, queues, buckets, jobs→uipath-platform. For context grounding / semantic search indexes→uipath-platform. For uip solution lifecycle→uipath-solution."
uipath-tasks
by UiPath
"UiPath Action Center human-in-the-loop tasks via uip tasks: list, assign, complete, plus task catalogs, comments, labels, metadata, and task data (get/save). For authoring HITL nodes in flows/agents→uipath-human-in-the-loop. For Orchestrator→uipath-platform, codedapp→uipath-coded-apps. Skip Document Understanding."
pr-review
by Gentleman-Programming
Reviews GitHub PRs and leaves human, direct comments. Trigger: When user asks to review a PR, check a PR, or gives a PR URL.
Documentation Standards
by HoangNguyen0403
Essential rules for code comments, READMEs, and technical documentation.
review-darling-arm64-contributions
by SlopDotCash
"Independently evaluate an xchemtina/darling-arm64 tier claim, upstream fix, falsified finding, flake analysis, or harness for architecture honesty, control discipline, A/B/A integrity, reproducibility, attribution, and contribution credit. Use in project CI or maintainer review before accepting work or changing a public reward allocation."
review-asi-contributions
by SlopDotCash
"Independently evaluate whether a SlopDotCash/asi contribution delivers a reproducible hill climb, measured research advancement or refutation, or an actual reproduced bug fix. Reject generic improvements, cleanup, and trivial work."
contribute-to-canonry
by SlopDotCash
Builds and verifies useful changes to Canonry, the agent-first open-source AEO platform. Use for a reproduced defect or a bounded maintainer issue in Canonry/canonry; excludes coverage farming, live provider spend, version-only bumps and unrelated projects.
contribute-to-darling-arm64
by SlopDotCash
"Raise a real macOS application one verified tier up the arm64 Darling ladder, fix a reproduced defect upstream in darlinghq, or falsify a recorded finding in xchemtina/darling-arm64. Every outcome ships a control, an A/B/A where it claims a fix, and a rerunnable harness. Use for measured arm64 capability, never for x86_64 work, refactors, or cleanup."
omero-integration
by jaechang-hits
"OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with tags and key-value pairs, manage ROIs, and integrate OMERO image data into downstream analysis pipelines — all programmatically without the OMERO desktop GUI."
anndata-data-structure
by jaechang-hits
"Annotated data matrices for single-cell genomics. AnnData stores expression data (X) with observation metadata (obs), variable metadata (var), layers, embeddings (obsm/varm), graphs (obsp/varp), and unstructured data (uns). Use for .h5ad/.zarr file handling, dataset concatenation, and scverse ecosystem integration. For analysis workflows use scanpy; for probabilistic models use scvi-tools."
etetoolkit
by jaechang-hits
"ETE Toolkit (ETE3) is a Python environment for phylogenetic tree analysis, manipulation, and visualization. Parse Newick/NHX/PhyloXML trees, traverse and annotate nodes, render publication-quality figures with TreeStyle/NodeStyle, integrate NCBI taxonomy for taxon-aware operations, and run PhyloTree workflows for comparative genomics. Use for building species trees, gene family evolution analysis, and annotated tree figures."
nnunet-segmentation
by jaechang-hits
"Train and deploy automated medical image segmentation models using nnU-Net's self-configuring framework that auto-selects optimal architecture, preprocessing, and training for any modality. Supports CT, MRI, microscopy, and ultrasound with 2D, 3D full-res, 3D low-res, and cascade configurations. Pipeline: convert dataset → plan and preprocess → train (5-fold cross-validation) → find best configuration → predict → ensemble. Use when classical segmentation fails and annotated training data is available."
napari-image-viewer
by jaechang-hits
"Interactive multi-dimensional image viewer for scientific microscopy data. Napari displays 2D/3D/4D arrays as Image, Labels, Points, Shapes, and Tracks layers; supports real-time annotation, plugin-based analysis, and headless screenshot export. Core visualization tool for bioimage analysis workflows. Use ImageJ/FIJI for macro-based processing; use napari for Python-native interactive visualization and plugin-based deep learning segmentation review."
ena-database
by jaechang-hits
"European Nucleotide Archive (ENA) REST API access for genomic sequences, raw reads, assemblies, and annotations. Portal API search with query syntax, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM download URLs, taxonomy queries, cross-references. For multi-database Python queries prefer bioservices; for NCBI-specific queries use pubmed-database or Biopython Entrez."