LLM Mart Basic

The Checkpoint Harmony Email (Avanan) whitelist and blacklist surface: the match fields and matching modes an exception accepts, the defaults that widen an entry beyond what was typed, the id mismatch between listing and editing, and the standing security consequence of a detecti

Discover and compare Jev and TypeSafe SDKs, integrations, applications, and evaluations. Use when selecting public resources for a typed-decision workflow or checking what evidence exists for a Jev claim.

Flint · local-skills-hub — a local-first personal AI skills asset manager. Centralize, tag, deduplicate skills, and deploy them into agent and project directori…

Inspect PDF, Microsoft Office (docx/xlsx/pptx and legacy doc/xls/ppt), and Apple iWork (key/numbers/pages) files without opening or rendering them. Use for page and slide and sheet counts, title/author/created metadata, encryption and macro and digital-signature and JavaScript ri

A coding agent harness built specifically for Motif-3

Build comprehensive chromatin accessibility maps by aggregating ATAC-seq and DNase-seq narrowPeak data across multiple ENCODE experiments, donors, and labs. Use when the user wants to answer "where is chromatin accessible in my tissue?" by combining peak calls into a union peak s

Guide for multi-experiment batch operations: QC screening, batch download, comparison, and report generation across many ENCODE experiments simultaneously. Use when users need to process 5+ experiments together, create experiment comparison tables, perform batch quality checks, o

Install bioinformatics tools for ENCODE data analysis. Covers CLI tools (BWA, STAR, samtools, MACS2), R/Bioconductor packages (DESeq2, Seurat, ChIPseeker), Python packages (Scanpy, deeptools), and Nextflow pipeline infrastructure. Generates conda environments, R install scripts,

Guide for integrating CellxGene Census single-cell data with ENCODE bulk experiments. Use when users need cell-type-specific expression context for ENCODE regulatory data, want to deconvolve bulk ENCODE signals, or validate regulatory elements at single-cell resolution. Trigger o

Generate proper ENCODE citations for publications, grants, and presentations. Use when the user needs to cite ENCODE data, create bibliography entries, write acknowledgment sections, or ensure compliance with ENCODE data use policy.

Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinica

Compare ENCODE experiments across different biosamples, tissues, or cell lines to identify tissue-specific regulatory patterns. Use when the user wants cross-tissue comparison, cell-type comparison, tissue-specific elements, differential chromatin, biosample matching, disease vs

Cross-reference ENCODE data with PubMed, bioRxiv, ClinicalTrials.gov, Open Targets, GTEx, ClinVar, GWAS Catalog, gnomAD, Ensembl, and other scientific databases. Use when the user wants to find publications, preprints, or clinical trials related to ENCODE experiments, chain ENCOD

Use ENCODE functional genomics data for disease mechanism research. Use when the user wants to connect GWAS variants to regulatory elements, annotate disease-associated loci with functional data, identify therapeutic targets from epigenomic data, build disease regulatory models,

Download ENCODE genomics files (BED, FASTQ, BAM, bigWig, etc.) to the user's machine. Use when the user wants to download data files from ENCODE experiments.

Query the Ensembl REST API for regulatory feature annotations, variant effect prediction (VEP), coordinate liftover, gene lookups, and cross-references. Use when the user needs to annotate variants with VEP (consequence, CADD, REVEL, SpliceAI), check Ensembl Regulatory Build over

Build comprehensive epigenomic profiles for tissues or cell types using ENCODE data. Use when the user wants to characterize chromatin states, assemble histone modification panels, create epigenomic landscapes, run ChromHMM segmentation, identify super-enhancers or bivalent domai

Analyze ENCODE functional genomics screens including CRISPR screens, MPRA (Massively Parallel Reporter Assays), and STARR-seq. Find screen data in ENCODE, process results, identify functional elements, and integrate with epigenomic annotations.

Search, query, and cross-reference NCBI GEO (Gene Expression Omnibus) datasets with ENCODE experiments. Use when the user wants to find GEO accessions for ENCODE experiments, search GEO for complementary datasets, download GEO metadata or series matrices, cross-reference ENCODE a

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene const

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

SMARTS arbitration — reconcile architectural artifacts against the scaffold and prior decisions; every variance resolved by an explicit, user-attributed choice.

Restructure code with behavioral parity proven through unmodified pre-existing tests, then refactor. No behavior change.

Cut a release the only sanctioned way — derive the target's declared version policy from the commit log, roll its changelog, compose an annotated tag, and optionally publish its exact declared assets. Takes the declared target's name as its only argument, or --dry-run to preview one with no write. The only path to a version tag.

Review a diff with the reviewer fleet, funneled to one triaged verdict. Targets the current working diff, a path, or an inbound GitHub PR.

Exploratory spike on a throwaway branch — answer a named question with disposable code. Never merges; exits to a findings note or {{CMD:feature}}.

Autonomous sprint — one interactive spec gate, then plan-to-PR execution with every auto-decision SMARTS-scored and logged. Hard gates remain true stops.

Daily repo hygiene — review the day's repo state, then perform the cleanups under per-action confirmation. Fast-forward only, never destructive without a yes.

Show the project's current state at a glance — stage, open tasks, open questions, overrides since the last checkpoint, current branch. Read-only.

Wire codeArbiter's statusline into ~/.claude/settings.json, or remove it.

The sanctioned task-board mutator — add a queued task, start one (flips to in-progress and stamps the date, minting a dotted ID on pick-up), or mark an in-progress task done. The only blessed write to open-tasks.md.

Opt-in lightweight STRIDE pass for a sensitive feature before implementation. Not a routine gate — invoke it when a change warrants security thought.

Deep, rarely-convened whole-codebase audit — eleven specialist lenses, a resumable on-disk audit log, findings filed as GitHub issues on approval. Expensive; estimates cost and STOPs before running. Never a required gate.

Watch a PR's CI to completion — diagnose on red, notify and offer the merge on green. Never auto-merges.

Copy a file OUT of a running sandbox box to the host — host-initiated egress only (docker cp). The reverse, a host→container bind, is impossible by construction.

Tear down a sandbox box — remove its container and named volume. --keep-volume leaves the volume; with no id, prune reclaims any leaked ca.sandbox=1-labeled object. Cached images are retained.

Run a single command inside a running sandbox box and capture a JSON result — exitCode, separate stdout/stderr, and a truncated flag past the byte cap. The scriptable exec seam.

Open an interactive shell inside a running sandbox box at /work/repo. Read-only root, non-root user, no host-FS access — explore the untrusted code interactively, then exit.

Pull an untrusted repo into an ephemeral, host-FS-isolated Docker container — clone into a named volume, build a dep-cached image, run under structural isolation. Network defaults to offline. Requires Docker and nixpacks.

Vet a new or changed third-party dependency for license, provenance, and supply-chain risk before any install runs.

Report the health of Architecture Decision Records — aged, unchallenged, supersession candidates, unresolved CONFIRM-NN. Read-only.

Atom Agent, Open-Source Governed AI Agent Platform for Self-Hosted Automation

The agent engineering intelligence harness, optimized tools, memory system, subagents and mixture of models packages ⚚

Sesori iOS/Android app and the Sesori Bridge CLI — drive Claude, Codex, OpenCode, Cursor, Pi, OMP, Hermes coding sessions from your phone

🧠 RepoBrain (formerly Antigravity) — Give your repo a brain. ChatGPT for your codebase: works in Claude Code, Cursor, Codex, Windsurf & more.

Use ChatGPT (Codex), Claude, and Grok (X Premium) subscriptions as DeepSeek Harness LLM providers — OAuth login in the web UI, no API keys

Latitude is the open-source AI monitoring platform.

Open-source AI browser agent for Chrome and Firefox (monorepo) 🧠

Official Model Studio CLI（阿里云百炼 CLI）built for AI Agent frameworks, exposing models, search, multimodal, and workflow capabilities as structured tool calls.

Curated DeepSeek Harness (DSH) plugins, extensions, tools, skills, clients, runtimes, integrations, and verified references — English and Chinese.

Turn papers, code, and docs into presentation-ready, natively editable PPTX in Codex / Claude Code. Native charts and equations, speaker notes, click-build anim…

Grix : Work with agents like talking to people.

Local First Ai Agent. Optimized for Local Ai models. Long context window. Proper tools callings. Runs privately on your device.

Model Context Protocol server that integrates AgentQL's data extraction capabilities.

AI that ships your tickets.

Metadata-driven CLI for AI Agent Bots — 48 operations across 7 domains, structured JSON envelope I/O, zero interactive prompts.

An open-source, extensible, self-hosted agent workspace with multi-runtime support for Codex, Claude Code, and more, plus reusable local apps for custom interfa…

Open-source Windows desktop client and GUI for DeepSeek Harness — zero-setup installer with Codex, plugins, skills, SSH, mobile remote access, and 11 skins.

The open-source AI workbench for scientific research

DeepSeek-native AI coding agent for your terminal. Engineered around prefix-cache stability — leave it running.

A Fully free agentic browser driver for AI , few tools, full control, real stealth, top-tier token efficiency.