What Do AI Agents Actually Change? An Empirical Taxonomy of Mutation Patterns in Performance-Improving Pull Requests

AI-agents (e.g., GitHub Copilot) collaborate as teammates in different software engineering tasks, including code generation proposed through pull requests (Agentic-PRs). For better agent efficiency, developers create instruction files that guide the AI-agents, including how to navigate the project, locate the right components, run tests, respect best practices, and more. In this paper, we investigate the relationship between the creation of these instructions and the performance of AI-agents in creating better pull requests, which have a higher chance of success (i.e., the merge rate), address more complex tasks (e.g., code churn), and require less effort to be merged (e.g., time to merge). To this end, we analyze 15,549 agentic PRs from 148 projects in the AIDev dataset. Using the three dimensions, we compare each project before and after the creation of the instruction files. We find that specifying instructions for AI-agents does not necessarily lead to better results. With the instruction files, 27.7% of the projects increased their merge rate by at least 20%, while 26.35% decreased it. The same observation is seen with the amount of changes (e.g., code churn, number of modified files) and with the efforts to merge an agentic PR (e.g., merge time and number of comments). From a first exploration, we find that projects that managed to increase their merge rate have substantially longer instruction files, which are also well structured into a higher number of sections and sub-sections. Our results motivate the need for research to assist practitioners in framing the development of instruction files as a software engineering activity (aka, \textbf{Instructions-as-Code}).

Pooled across five AI coding agents, pull requests (PRs) with a human Co-Authored-By trailer merge less often than purely-autonomous ones (53.8% vs. 79.8%) -- yet this aggregate finding is a textbook Simpson's Paradox. Stratifying 33,596 PRs from the AIDev dataset by agent identity reverses the conclusion: Copilot and Devin show large positive within-agent gaps (+41.2 and +33.5 pp, both p<0.001), while Cursor, Claude Code, and Codex show small effects whose cross-sectional 95% CIs span zero. The paradox is driven entirely by agent composition: Codex, which dominates 64.9% of the dataset, achieves high merge rates while rarely using co-authorship. But Simpson's Paradox is only the first layer of a cascade of confounders: within-repo controls eliminate Devin's gap (+33.5 to +1.6 pp, p=0.73); a commit-count control further halves Copilot's within-repo gap (+36.2 to +24.4 pp); restricted to multi-commit PRs, the Copilot within-repo effect dissolves to +4.8 pp (p=0.59). No agent retains a clear co-authorship effect once both repository selection and PR structure are controlled. Our findings caution against reporting agent-pooled statistics without stratification and demonstrate that cross-sectional co-authorship associations are largely selection and PR-structure artefacts rather than evidence of a causal benefit.

Scaling coding agents requires a continuing supply of executable data for training, benchmarking, and continuous evaluation. Each task must couple a realistic software state with a specification, development tools, and reliable verification. To expand this supply, we present Change2Task, a system grounded in repository history that converts merged pull requests into verified tasks on healthy modern revisions of the same repository. It aligns historical evidence with evolved code, reconstructs task states through Patch Reversal, Code Mapping, or Agent Reconstruction, and validates the lifecycle from a healthy base to a task state and a restored state. By deriving multiple tasks grounded in developer evidence from maintained environments, Change2Task provides executable data for coding agent training and evaluation while reducing repeated environment setup, storage, and task construction effort. We evaluate the system through five common and widely adopted coding agent task families: Bug Fix, Feature Addition, Test Generation, Application Programming Interface Migration, and Security Repair. Starting from 1,130 source changes eligible for construction, Change2Task achieves 79.6% verified task construction success across these task families. On a matched candidate set, it recovers 29.2% more verified tasks than a construction baseline based on pull requests. Historical and reconstructed cases achieve up to 98.0% matched outcome agreement under agent evaluation, while reuse of modern bases reduces measured expenditure across the complete pipeline by 10.8%.