docs(migration): maintainer handoff ultraplan, taxonomy, and upstream…

[hyperpolymath]

…… (#92)

…-slice kit (#82)

Summary

Establishes the strategic, technical, and operational roadmap for transitioning contributions from the hyperpolymath/MetaManifold-WebUI fork back to upstream maintainer Joshua Jewell (JoshuaJewell/MetaManifold-WebUI), directly addressing his feedback on upstream PR #13.

What this PR adds

1. Maintainer Handoff Ultraplan (docs/migration/ULTRAPLAN-MAINTAINER-HANDOFF.md):

• Retraction of PR chore(ci): remove Codecov residue — coverage now local artifact #13: Diagnosis of the 159 merge conflicts (merge base reverted to January root commit 06d85ba after git-filter-repo dead-asset cleanup) and exact closure command + drafted comment for Joshua.
• Maintainer Profile: Ground rules respecting veterinary science workflows, microbiome amplicon analysis priorities, and team bandwidth.
• 8-Track Taxonomy: Clear classification across Pipeline Fixes, Biological QC, Benchmarks, Statistics Cluster, Test Organization, React UI, Architectural Hard Calls, and Formal Evidence.
• 'Free' vs 'Hard Decision' Trade-Off Matrix: High-clarity breakdown showing what is safe/additive vs what requires architectural choice (YAML vs KYAML, Estate CI vs simple CI, React vs Stipple, exact math vs canonical R pipeline).
• R-Pipeline Protection & Dual-Track CI/CD: Guarantees that canonical biological tools (dada2, vegan, MASS::glm.nb) remain the primary blocking ground truth.
• Phased PR Sequencing: Atomic clean-branch roadmap re-anchored on ecefb1c (upstream main) with zero conflicts and zero Stipple/Vue dependencies.

2. Automated Upstream Slicing Kit (scripts/prepare-upstream-slices.sh):
   • Fetches upstream/main (ecefb1c).

• Generates four atomic, conflict-free branches directly from ecefb1c in temporary worktrees:
• upstream-slice/01-qc-and-fixes (FastQC/MultiQC in CI + 1x1 matrix & zero-depth fixes, 6 files)
  • upstream-slice/02-benchmarks (bench/ suites, 16 files)
• upstream-slice/03-statistics-cluster (real models, exact offsets, test renames, 16 files)
• upstream-slice/04-frontend-polish (accessible dialogs, TS types, 13 files)
  • Excludes ui/ and all Genie/Stipple dependencies completely.
  • Verifies zero merge conflicts against upstream main.

Hygiene & Conformance

• scripts/check-spdx.sh: OK (361 files covered).
• scripts/check-format.sh: OK (465 files checked).

Summary

Base check

• Base is hyperpolymath/MetaManifold-WebUI:main (not the upstream parent; application changes go to JoshuaJewell/MetaManifold-WebUI)

Changes

Engineering checklist

Required

• bun run check passes (frontend/: typecheck 0 errors, tests, benchmarks)
• scripts/check-spdx.sh / check-format.sh / check-lint.sh pass (advisory in CI — does not block merge)
• Conventional commit subjects (see CONTRIBUTING.md; advisory in CI)
• New source files carry the correct SPDX header (NOTICE explains the authorship rule)
• No secrets, credentials, .env, or sequencing data included
• No application-logic changes hidden inside alignment/tooling PRs

As applicable

• CHANGELOG.md updated for user/developer-visible changes
• docs/types/architecture.md updated if type boundaries moved
• docs/testing/coverage.md updated if test coverage moved
• New dependencies reviewed for licence compatibility
• docs/reproducibility.md updated if environment requirements changed

Testing

Summary

Base check

• Base is hyperpolymath/MetaManifold-WebUI:main (not the upstream
  parent; application changes go to JoshuaJewell/MetaManifold-WebUI)

Changes

Engineering checklist

Required

• bun run check passes (frontend/: typecheck 0 errors, tests,
  benchmarks)
• scripts/check-spdx.sh / check-format.sh / check-lint.sh pass
  (advisory in CI — does not block merge)
• Conventional commit subjects (see CONTRIBUTING.md; advisory in CI)
• New source files carry the correct SPDX header (NOTICE explains
  the authorship rule)
• No secrets, credentials, .env, or sequencing data included
• No application-logic changes hidden inside alignment/tooling PRs

As applicable

• CHANGELOG.md updated for user/developer-visible changes
• docs/types/architecture.md updated if type boundaries moved
• docs/testing/coverage.md updated if test coverage moved
• New dependencies reviewed for licence compatibility
• docs/reproducibility.md updated if environment requirements changed

Testing

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Note

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⚙️ Run configuration

Configuration used: Organization UI

Review profile: ASSERTIVE

Plan: Advanced

Run ID: 7b778df9-60ce-4d12-83d2-f1439207c49c

📥 Commits

Reviewing files that changed from the base of the PR and between 55d6608 and 253be84.

📒 Files selected for processing (2)

• docs/migration/ULTRAPLAN-MAINTAINER-HANDOFF.md
• scripts/prepare-upstream-slices.sh

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✨ Finishing Touches

📝 Generate docstrings

• Commit to this branch
• Create a new PR

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