Traceable Scholarship: Page Anchors and Ariadne's Thread for Humanistic Inquiry in the Age of Generative AI

F(AI)2R is FAIR research with AI in the loop, twice: an AI-assisted authoring pass and a machine-readable audit pass over every artefact. AI systems now draft, refactor, and verify research artefacts, yet their contributions are rarely recorded in a form a later human or machine can audit. Building on the original F(AI)2R experiment, we generalize its provenance model beyond scholarly writing into aiprov, a PROV-O extension covering any AI-in-the-loop artefact, and we package the method as an executable skill that an AI agent operates itself: setup asks the human operator for their ORCID ID, resolves their identity from the public registry, and scaffolds continuous integration that gates every push on graph conformance and publishes the current build of this very paper. The paper is its own case study. Every activity, claim, and source in its production is recorded in the repository's provenance graph under two invariants: no parentless claim, and verification rungs that only humans may grant.

AI-assisted research is crossing a threshold: fully automated systems can now generate research papers for as little as $15, while long-horizon agents can execute experiments, draft manuscripts, and simulate critique with minimal human input. Yet this productivity frontier exposes a deeper integrity problem: under scientific pressure, even frontier LLMs still fabricate results, miss hidden errors, and fail to judge novelty reliably. Studying developments through April 2026, we present an end-to-end analysis of AI across the complete research lifecycle, organized into four epistemological phases: Creation (idea generation, literature review, coding & experiments, tables & figures), Writing (paper writing), Validation (peer review, rebuttal & revision), and Dissemination (posters, slides, videos, social media, project pages, and interactive agents). We identify a sharp, stage-dependent boundary between reliable assistance and unreliable autonomy: AI excels at structured, retrieval-grounded, and tool-mediated tasks, but remains fragile for genuinely novel ideas, research-level experiments, and scientific judgment. Generated ideas often degrade after implementation, research code lags far behind pattern-matching benchmarks, and end-to-end autonomous systems have not yet consistently reached major-venue acceptance standards. We further show that greater automation can obscure rather than eliminate failure modes, making human-governed collaboration the most credible deployment paradigm. Finally, we provide a structured taxonomy, benchmark suite, and tool inventory, cross-stage design principles, and a practitioner-oriented playbook, with resources maintained at our project page.

AI research pipelines can now generate academic work that may satisfy existing peer review standards for quality, novelty, and methodological rigor. However, the publication system was built around the assumption that research is produced by human authors. It therefore lacks a clear way to evaluate work when the knowledge claim may be valid but the producer is partly or fully automated. This paper proposes a two-layer certification framework for AI-generated research. The first layer evaluates whether the knowledge claim is sound. The second layer evaluates the level of human contribution. This separation allows journals and conferences to assess pipeline-generated work more consistently without creating new institutions. The framework uses normative analysis, conceptual design, and dry-run validation against representative submission cases. It classifies human contribution into three categories: Category A, where the work is reachable by an automated pipeline; Category B, where human direction is required at identifiable stages; and Category C, where the work goes beyond current pipeline capability, especially at the problem-formulation stage. The paper also proposes dedicated benchmark slots for fully disclosed automated research. These slots would provide a transparent publication path and help reviewers calibrate judgments over time. The key argument is that publication has historically certified two things at once: that the knowledge is valid and that a human produced it. AI research pipelines separate these two claims. By decoupling knowledge certification from authorship attribution, the proposed framework responds to a structural change already underway. It can be implemented within existing editorial systems, works even when attribution is uncertain, and recognizes human frontier contribution based on epistemic value rather than human origin alone.