The paper introduces Aleena, an open-source lifecycle alignment agent for research software engineering collaborations. It addresses how decisions and their rationale become fragmented across Slack, meetings, GitHub issues, and pull requests, causing researchers and software engineers to develop divergent views of intent, ownership, and scientific assumptions. Aleena uses GitHub as a shared collaboration surface and converts multimodal stakeholder interactions into structured project records. These records are intended to surface risks, track open questions, and preserve decision continuity while keeping human stakeholders responsible for decisions. The paper presents the motivation, system design, prototype, and illustrative lifecycle scenarios grounded in university-based research software engineering center experiences.
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