docs(migration): maintainer handoff ultraplan, taxonomy, and upstream-slice kit

[arena-ai-coding-agent]

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).

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