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Governance And Cross-Repository Boundaries

Source: GOVERNANCE.md

This document records the first-pass governance boundaries for the floundeR revival. It is intentionally practical: agents should inspect these files before making cross-repository changes.

floundeR

No canonical floundeR product charter was found in ../mnemosyne-docs during the 2026-06-13 baseline review. Until one is authored, this repository’s governing local files are:

  • AGENTS.md
  • ROADMAP.md
  • TODO.md
  • DATASETS.md
  • DERIVED_POD5_DEMOS.md
  • DISTRIBUTION.md
  • BIOCONDUCTOR_POLICY.md
  • GITHUB_INSTALLATION.md
  • REPORTING_INTERFACE.md
  • GRAMMATEUS_RUNTIME_INTERFACE.md
  • GRAMMATEUS_RELEASE_ASSETS.md
  • LEGACY_REPORTING.md

pod5-tools

No canonical pod5-tools product charter was found in ../mnemosyne-docs during the 2026-06-13 baseline review. Until one is authored, inspect:

  • ../pod5-tools/AGENTS.md
  • ../pod5-tools/README.md
  • ../pod5-tools/roadmap.md
  • ../pod5-tools/todo.md

Only the subset of pod5-tools needed for nanopore QC, review, provenance, demonstration datasets, reporting, and synoptikon handoff should be exposed through floundeR.

Bamana

No canonical Bamana product charter was found in ../mnemosyne-docs during the 2026-06-13 baseline review. Until one is authored, Bamana integration is governed by:

  • ../bamana/CHARTER.md
  • ../bamana/docs/project-charter.md
  • ../bamana/docs/json-output.md
  • Bamana’s public schemas/examples where present

Only BAM/BGZF/FASTQ behavior that directly supports nanopore QC, review, provenance, reporting, and synoptikon handoff should be surfaced in floundeR.

Porkchop

No canonical Porkchop product charter was found in ../mnemosyne-docs during the 2026-06-13 baseline review. Until one is authored, Porkchop integration is governed by:

  • ../porkchop/AGENTS.md
  • ../porkchop/ROADMAP.md
  • ../porkchop/README.md
  • ../porkchop/docs/output/json.rst
  • ../porkchop/docs/kits/provenance.rst
  • ../porkchop/docs/validation/index.rst

Only adapter, primer, barcode, kit-registry, cDNA, and library-preparation evidence that directly supports nanopore QC, review, provenance, reporting, and synoptikon handoff should be surfaced in floundeR.

Grammateus

Grammateus has canonical documentation in ../mnemosyne-docs. Inspect at least:

  • ../mnemosyne-docs/charters/products/grammateus/GRAMMATEUS_CHARTER.md
  • ../mnemosyne-docs/requirements/srs/products/grammateus/GRAMMATEUS_SRS.md
  • ../mnemosyne-docs/products/grammateus/GRAMMATEUS_RENDERING_ELEMENTS_CONTRACTS.md
  • ../mnemosyne-docs/products/grammateus/GRAMMATEUS_TRUSTED_REPORT_LIFECYCLE_CONTRACTS.md
  • ../mnemosyne-docs/products/grammateus/GRAMMATEUS_TRUSTED_REPORT_SYNOPTIKON_CONTRACTS.md

Grammateus should provide report element, provenance, rendering, and trusted report semantics. floundeR should not create a parallel report trust stack. Grammateus source code is private. floundeR must therefore interact with Grammateus through optional, prebuilt, verified runtime/reporting artifacts or through authorized private development checkouts, not by making private source a mandatory dependency of the open-source package.

Synoptikon And Mneion

Synoptikon-facing work is expected to land through ../mnemosyne. The relevant canonical Mneion control-plane documents in ../mnemosyne-docs include:

  • ../mnemosyne-docs/charters/products/mneion/MNEION_CHARTER.md
  • ../mnemosyne-docs/requirements/srs/products/mneion/MNEION_SRS.md
  • ../mnemosyne-docs/architecture/ards/products/mneion/ARD-001-mneion-architecture-review.md

Any QC payload, report lifecycle, signing, or governance workflow must preserve those boundaries and reuse existing Synoptikon/Mneion identity, role, authority-key, audit, and governance-signing patterns.

Generated Documentation Policy

During normal development, source documentation should be edited first and generated artifacts should be refreshed intentionally. The repository may keep generated man/ files because they are part of normal R package development. Generated docs//pkgdown output should be treated as release-oriented output: update it when public documentation is intentionally refreshed, but do not let stale generated pages drive source behavior.

Root-level project-control files such as AGENTS.md, ROADMAP.md, TODO.md, DATASETS.md, DERIVED_POD5_DEMOS.md, DISTRIBUTION.md, BIOCONDUCTOR_POLICY.md, GITHUB_INSTALLATION.md, REPORTING_INTERFACE.md, GRAMMATEUS_RUNTIME_INTERFACE.md, GRAMMATEUS_RELEASE_ASSETS.md, LEGACY_REPORTING.md, and this file are repository governance files. They are excluded from R source package builds through .Rbuildignore.