Dependency-aware, Dolt-backed issue tracker built for AI coding agents that survive context loss
Cognition | Agent Trace: Capturing the Context Graph of Code
We’re excited to join in Cursor, Cloudflare, Vercel, git-ai, OpenCode and others in support of [Agent Trace](https://agent-trace.dev/). As described in the spec, Agent Trace is an open, vendor-neutral spec for recording AI contributions alongside human authorship in version-controlled codebases.
kenn-io/kata
Local-first issue tracking for AI-assisted software work, with an agent-friendly CLI and human-facing TUI
Git AI - Track AI Code all the way to production
Cross-agent observability from prompt to production. Track AI-generated code from Cursor, Claude Code, GitHub Copilot, Gemini, and more through the entire SDLC.
SWE-Bench Pro: Can AI Agents Solve Long-Horizon Software Engineering Tasks?
Large Language Model (LLM) agents have been widely adopted in modern software development workflows. SWE-bench [13] and related works [23, 24, 22, 25, 15] establish the task of issue resolution as a de-facto standard for assessing their capability and usefulness. In this setting, an agent is given an entire codebase, a task description (e.g., a bug report or feature request) in natural language and is instructed to produce a code patch that resolves the issue and passes the repository’s test suite. These benchmarks have been instrumental in demonstrating both the substantial potential and the persistent limitations of current models as SWE agents.
Evaluating AGENTS.md: Are Repository-Level Context Files Helpful for Coding Agents?
A widespread practice in software development is to tailor coding agents to repositories using context files, such as AGENTS.md, by either manually or automatically generating them. Although this practice is strongly encouraged by agent developers, there is currently no rigorous investigation into whether such context files are actually effective for real-world tasks. In this work, we study this question and evaluate coding agents' task completion performance in two complementary settings: established SWE-bench tasks from popular repositories, with LLM-generated context files following agent-developer recommendations, and a novel collection of issues from repositories containing developer-committed context files. Across multiple coding agents and LLMs, we find that context files tend to reduce task success rates compared to providing no repository context, while also increasing inference cost by over 20%. Behaviorally, both LLM-generated and developer-provided context files encourage broader exploration (e.g., more thorough testing and file traversal), and coding agents tend to respect their instructions. Ultimately, we conclude that unnecessary requirements from context files make tasks harder, and human-written context files should describe only minimal requirements.
The issue tracker that runs inside the loop.
A local-first issue tracker for coding agents and the humans steering them. Queries in 4ms, on your own machine.
Agent READMEs: An Empirical Study of Context Files for Agentic Coding
Agentic coding tools receive goals written in natural language, break them down into specific tasks, and write or execute code with minimal human intervention. Central to this process are agent context files (e.g., AGENTS.md and CLAUDE.md) that provide persistent, project-level instructions. In this paper, we conduct the first large-scale empirical study of 2,303 agent context files from 1,925 repositories to characterize their structure, maintenance, and content. We find that these files are not static documentation but complex, difficultto-read artifacts that evolve like configuration code through frequent, small additions. Our content analysis of 16 instruction types shows that developers prioritize functional context, such as test procedures (75.9%), implementation details (70.8%), and architecture (68.1%). We also identify a significant gap: non-functional requirements such as security (14.8%) and performance (14.5%) are rarely specified. These findings indicate that while developers use context files to make agents functional, they provide few guardrails to ensure that agent-written code is secure or performant, highlighting the need for improved tools and practices.
In software, the code documents the app. In AI, the traces do.
Discover how traces for documentation replace code as the source of truth for AI agents. Learn to debug, test, and optimize agent behavior effectively.
Agent Plugins
A portable package format for reusable components that extend AI agents.
Reimagining research papers as interactive and reliable AI agents
Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper’s code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent’s effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome1 to interpret genomic variants and agents based on Scanpy2 and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)3 to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.
Reimagining research papers as interactive and reliable AI agents
Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper’s code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent’s effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome1 to interpret genomic variants and agents based on Scanpy2 and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)3 to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.
The 2025 AI Agent Index Documenting Technical and Safety Features of Deployed Agentic AI Systems
Agentic AI systems are increasingly capable of performing professional and personal tasks with limited human involvement. However, tracking these developments is difficult because the AI agent ecosystem is complex, rapidly evolving, and inconsistently documented, posing obstacles to both researchers and policymakers. To address these challenges, this paper presents the 2025 AI Agent Index. The Index documents information regarding the origins, design, capabilities, ecosystem, and safety features of 30 state-of-the-art AI agents based on publicly available information and email correspondence with developers. In addition to documenting information about individual agents, the Index illuminates broader trends in the development of agents, their capabilities, and the level of transparency of developers. Notably, we find different transparency levels among agent developers and observe that most developers share little information about safety, evaluations, and societal impacts. The 2025 AI Agent Index is available online at https://aiagentindex.mit.edu.
How to harness AI
"Coding agents" are complicated but intelligible
Managing Agent Skills with Your Package Manager | pavel.pink
AI coding agents use skills — markdown files that teach them domain-specific tasks. We publish ours as conda packages and manage them with pixi, getting versioning, lockfiles, and supply chain security for free.
