Quality-Driven Agentic Reasoning for LLM-Assisted Software Design: Questions-of-Thoughts (QoT) as a Time-Series Self-QA Chain

Qualitative analysis plays a pivotal role in understanding the human and social aspects of software engineering. However, it remains a demanding process shaped by the subjective interpretation of individual researchers and sensitive to methodological choices such as prompt design. Recent advancements in Large Language Models (LLMs) offer promising opportunities to support this type of analysis, although their reliability in reproducing human qualitative reasoning under varying prompting conditions remains largely untested. This study presents a controlled empirical evaluation of three LLMs -- Claude Haiku, DeepSeek-Chat, and Gemini 2.5 Flash -- across two prompt engineering strategies (zero-shot and multi-shot closed coding), using Cohen's kappa as the primary agreement metric over ten independent runs per configuration. Results suggest that multi-shot prompting significantly improves agreement for Claude Haiku (Delta kappa = +0.034, Wilcoxon p = 0.004) but not for DeepSeek-Chat or Gemini 2.5 Flash. Intra-model stability varies substantially -- DeepSeek-Chat and Claude Haiku exhibit the lowest variance (SD approx. 0.017), while Gemini 2.5 Flash is the least stable (SD = 0.038). A systematic over-prediction of "Sharing Negative Feedback" is identified across all models (bias ratios up to 5.25x), alongside consistent under-prediction of "Expressing Concerns." Collectively, these findings provide empirical evidence for prompt engineering guidelines in LLM-assisted qualitative coding for software engineering research.

Large language models (LLMs) are widely used for open-ended tasks, but underspecified prompts can lead to low-quality answers and additional interaction. This paper studies whether structured prompt design improves response quality while reducing user effort. We compare three prompt conditions: a raw prompt, a checklist-improved prompt, and a clarifying-question prompt. We evaluate these conditions across four task types--summarization, planning, explanation, and coding--using three LLM systems: ChatGPT, Claude, and Grok. Each output is scored with a unified rubric covering task completion, correctness, compliance, and clarity. Checklist-improved prompts achieved the highest mean rubric score, 7.50 out of 8, compared with 5.67 for raw prompts and 6.67 for clarifying-question prompts. Checklist prompts also produced the best quality-effort tradeoff, using fewer average tokens than both raw and clarifying prompts. These results suggest that a simple prompt checklist can improve LLM responses while reducing unnecessary interaction.

Coding agents, autonomous systems that use large language models (LLMs) to resolve software engineering tasks, rely on agentic scaffolding: a middleware layer in between a developer and a large language model that orchestrates system prompts, tool execution, context management, and iterative reasoning loops. While these scaffoldings evolve at extreme velocities, no study has examined how this evolution affects agent quality (i.e., effectiveness and efficiency) over time. Practitioners regularly report quality regressions after scaffolding updates, yet consistently attribute them to the underlying model rather than the scaffolding itself. In this paper, we address this gap by conducting the first controlled longitudinal study that isolates the scaffolding's contribution. Unlike prior work that fixes the scaffolding and varies the model, we fix the model and vary only the scaffolding, evaluating 35 sequential releases to measure their impact on agent effectiveness and efficiency. We first empirically study the development and release evolution of five major open-source scaffoldings (i.e., Codex, Qwen Code, Gemini, OpenCode, and OpenHands), revealing extreme release velocities exceeding two releases per day and thousands of issues within months. We then perform a controlled deep dive into 35 sequential releases of the Qwen Code CLI, evaluating each against 50 stratified SWE-bench Verified tasks while holding the underlying LLM constant. We trace the resulting quality fluctuations to specific development patterns and architectural components, and illustrate our findings with concrete qualitative evidence linking individual pull requests to measured quality shifts.