Covers operating AI coding agents securely: auditing whether the agent runs sandboxed, permission and dangerous-command configuration, containerized environments, secrets kept out of context, network egress and token privileges, prompt-injection risk, and the privacy of agent use itself. Use PROACTIVELY when permission gating is broadly disabled (skip-permissions modes), when secrets are visible to the agent's shell, or when the agent processes untrusted code, issues or web content; when a project holds personal or confidential data while a cloud agent is active (what leaves the machine, retention, training use), or when the user asks how to run coding agents safely or privately. (Supply-chain security: rseng-security; disclosing agent contributions: rseng-ai-declaration.)

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Covers declaring AI involvement with the AI Declaration Format (https://ai-declaration.org): creating and maintaining an aidecl.yaml that records which AI tools and agents were used, what each contributed, when and how much, plus the README disclosure footnote, JSON/JSON-LD export and CI validation. Machine-readable disclosure is the practice; this format is one implementation. Use PROACTIVELY when an AI assistant or agent creates or modifies a project's content - generate aidecl.yaml if missing, update it after AI-assisted changes. Also use when the user asks about AI transparency, provenance, disclosure or EU AI Act disclosure, wants to state that NO AI was used, or mentions aidecl. For concealment requests see rseng-honesty; for the human review duty see rseng-human-verification.

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Covers long-term archiving of research software and data: Software Heritage save requests and SWHID persistent identifiers, Zenodo deposits with versioned DOIs and forge integration, choosing domain and institutional repositories, deciding what to archive (code, data, environments, documentation) and when, and archiving at project retirement. Use when the user wants software or data preserved beyond the life of a forge account, grant or lab, mentions Software Heritage, SWHIDs, Zenodo deposits or archiving, retires or hands over a project, prepares artifacts that must stay resolvable for a paper, or when funder policy requires long-term preservation. (Cutting the release itself is rseng-publishing-releasing; day-to-day data storage and repository choice is rseng-data-management.)

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Covers processing research data that outgrows one machine's memory: out-of-core and chunked computation, Dask for scaling the scientific Python stack, Spark for distributed tabular pipelines, lazy evaluation, partitioning strategies, idempotent and restartable batch jobs, and knowing when NOT to distribute. Use when datasets no longer fit in memory, when the user mentions Dask, Spark, out-of-core or larger-than-memory data, when a pandas/NumPy workflow hits memory limits, or when designing batch pipelines over many files. (Cluster job submission and job arrays are rseng-hpc-computing; pipeline orchestration engines are rseng-workflows; profile first with rseng-performance-profiling.)

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Covers continuous integration and delivery for research software: CI/CD concepts, automating builds and tests with GitHub Actions and GitLab CI/CD, and wiring an organization's GitLab CI infrastructure to a GitHub-hosted project. Use when the user asks to set up CI, write a pipeline or workflow file (.github/workflows, .gitlab-ci.yml), add automated builds/tests on push or pull request, publish a package or deploy docs when a tag or release is cut, cache dependencies to speed up CI runs, choose between GitHub Actions and GitLab CI, use self-hosted or GPU runners, mirror a repo, or report external CI status back to GitHub. For what to test and shrinking a test matrix see rseng-testing; for linter and pre-commit policy see rseng-code-quality.

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Covers verifying that every citation is real, correct and current: checking references in manuscripts, READMEs, references files and code metadata against Crossref and OpenAlex, screening cited DOIs against the Retraction Watch database, catching fabricated or mis-attributed citations (a documented AI failure mode), and keeping bibliographies and CITATION.cff files resolvable. Use PROACTIVELY before any bibliography, reference list or citation metadata is finalized or published, whenever the agent itself has produced citations, and when the user asks to check references, mentions broken DOIs, retracted papers or citation verification, or prepares a manuscript, README or software paper with references. (Making your own software citable is rseng-citation-metadata.)

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