Contemporary LLM-based coding agents produce code as black-box outputs: the rationale behind each line is hidden, the evolution of the code through benchmark-driven repair is ephemeral, and post-hoc auditing is impossible. We present a code generation concept that addresses these shortcomings through three complementary mechanisms: (i) a relational snippet-history schema that records, per repair event, the benchmark reference, round number, failure text, and LLM explanation, enabling full provenance queries; (ii) a browser-based visualisation tool that renders this history as heat-mapped, hover-annotated source code; and (iii) a competitive fractional position-key indexing scheme with tree-node delimiters that assigns stable, lexicographically-ordered identifiers to each code snippet, enabling fine-grained tracking without disrupting surrounding lines. We evaluate TraceCoder on 30 algorithmic programming tasks spanning string processing, mathematical computation, and data-structure manipulation, across two provider configurations. Of these, 10 exhaust the 6-iteration budget on tasks with subtle edge-case behaviour. Mean Chg% reaches 30%, three in ten code snippets carry a traceable repair-event row, compared to 21% when using Gemini 2.0 Flash as sole provider on a 20-task subset. Three detailed case studies demonstrate how the system explains which specific benchmark failures shaped each line of the final program. The proposed mechanism makes the internal "narrative" of automated code generation auditable and replayable, a property essential for trust and accountability in production deployments.
In this paper, we describe LLMoxie, an institutional AI platform whose three-tiered architecture supports multi-cloud and on-premise inference, a LiteLLM/MLflow control plane for authentication, budgeting, PII masking, and observability, and an application augmentation layer for AI coding agents. Layered on top, an open-source RSE-Plugins ecosystem encodes accumulated RSE knowledge as a Plugin-Agent-Skill hierarchy spanning scientific Python practice, domain-specific knowledge, a six-phase research-and-implement workflow, and project lifecycle management. Scientific software is judged less by raw code quality than by whether it can be cited, audited, reproduced, and extended. Off-the-shelf AI coding agents, optimized against commercial software benchmarks, are poorly calibrated for this setting: they ignore the conventions of the scientific Python libraries they invoke, mishandle sensitive or embargoed data, and leave decision trails that are difficult to reconstruct after the fact. We report on twenty months of practice at a university-based research software engineering (RSE) center, where RSEs embedded across astronomy, earth and climate science, agriculture, and health projects worked to close this gap. We characterize the recurring infrastructure, governance, and process challenges of adopting Agentic AI inside a multi-domain RSE center, describe the platform and plugin design, and distill operational lessons from real scientific software deployments. Together, the platform and plugins shift AI coding agents from generic code generators into domain-aware collaborators that respect community norms and produce auditable provenance of technical reasoning.