Soei: Structured Observability of Evidence and Intent for Multi-Agent AI Software Engineering

AI coding agents are commonly evaluated as models but deployed as systems. Their reliability depends not only on model capability, but on the harness, execution state, retrieval, memory and state management, permissions, review interfaces, and resource allocation. This monograph examines those boundaries and develops a framework for evaluating and operating coding agents reliably. It synthesizes 164 scholarly works, 100 practitioner records, 29 benchmark records, and 17 author-system case records through a structured multivocal review, targeted update audits, software-engineering coverage analysis, and distributed-systems evidence synthesis. Across this evidence, many apparent model failures originate elsewhere in the system, while improvements at one layer often fail to propagate to end-to-end outcomes. Evaluation and operation are treated as a dependency chain in which weaknesses in task construction, execution environments, retrieval, state management, verification, or observability can invalidate downstream conclusions. The monograph contributes a versioned catalog of 206 reliability records: 193 gated practices, including 56 developed in depth, plus 13 research leads; an evidence ledger; a framework for dependency and repair asymmetry across the agent lifecycle; measurements and failure cases from operated agent systems; runnable evaluation and reliability protocols; and five reusable agent skills with evidence maps. Together, these provide a system-level methodology for distinguishing model capability from infrastructure effects, designing defensible evaluations, and building systems that recover safely when components fail. The review is structured rather than exhaustive, evidence strength varies by topic, and results depend on workload and configuration. The methods record which search lanes were executed, which remain unexecuted, and limits on evidence-grading claims.

AI coding agents increasingly act directly within software environments, yet existing analyses of their failures rely on benchmark trajectories that miss how developers actually experience misalignment. We present an observational study of 20,574 coding-agent sessions from 1,639 repositories across IDE and CLI workflows. We operationalize misalignment as a breakdown made visible through developer pushback, and annotate each episode along four axes: form, cause, cost, and resolution. We identify seven recurring forms, spanning how agents read projects, interpret developer intent, follow rules, bound their actions, implement and execute code, and report progress. 90.50% of episodes impose effort and trust costs rather than irreversible system damage, yet 91.49% of visible resolutions still require explicit user correction. Misalignment patterns also differ across IDE and CLI settings, persist across adjacent sessions, and shift over time: while overall rates decline, constraint violations and inaccurate self-reporting grow in share. Our findings inform the design of training, evaluation, and interfaces for keeping coding agents aligned with real developer workflows.

Coding agents are increasingly evaluated not only by whether they solve a task, but also by how they execute it. However, existing process-level evaluations often treat action prediction, task uncertainty, and step attribution as if they were the same problem, which makes it unclear what such evaluations actually measure. In this paper, we introduce a measurement framework for process evaluation in coding agents and instantiate step-level causal attribution with SCAE, a replay-based estimator derived from a structural causal model of agent execution. Our framework combines prefix-conditioned identification, replay/intervention-based estimation, and controlled judge-information manipulation to study process evaluation at the action, task, and step levels. Experiments on 499 file-localization episodes from 12 repositories show that next actions are driven primarily by execution provenance rather than code-graph transitions, execution uncertainty is structured at the task rather than step level, and full-trace judges exhibit systematic collider bias, suggesting that current process evaluation often measures semantic relevance rather than certified causal contribution.