Restructure repository for Phase 2

[PraneethMerugu]

What changed

• promotes PottsToolkit to the root package and removes the temporary Potts umbrella
• gives CorePotts, MakiePotts, and NeuralPotts independent package tests
• separates cross-package tests into an explicit integration/ environment and records the known chemotaxis-fragmentation defect without representing it as green
• reorganizes CorePotts source by stable responsibilities while preserving the scientific implementation
• prunes runtime dependencies, adds complete compat bounds, and pins KernelIntrinsics to the approved Metal-support fork commit
• establishes reproducible paper, docs, examples, notebook, dashboard, and benchmark environments
• adds a machine-enforced repository structure contract
• rewrites CI around independent package, integration, native ARM64/x86_64, and GPU qualification

Why

This establishes the package boundaries and repository architecture required before semantic and performance refactoring. It prevents the old umbrella structure, dependency leakage, and mixed test ownership from becoming part of the public API.

Impact

This is intentionally breaking pre-release work. Users now load PottsToolkit directly. No migration layer is included because the API is not yet released.

Qualification (Julia 1.12.6)

• PottsToolkit, CorePotts, MakiePotts, and NeuralPotts pass independently
• thermodynamics, biophysics, and cross-package integration shards pass
• native CPU verification passes on macOS ARM64 and Linux x86_64
• real-device Metal and AMDGPU/ROCm validation passes
• CPU benchmark smoke passes for sequential, lottery, and checkerboard
• local real-device Metal benchmark smoke passes for lottery and checkerboard
• documentation build, repository structure validator, and required aggregate pass

CUDA is intentionally skipped until a CUDA runner is enabled. The Phase 2 real-GPU exit gate is satisfied independently by Metal and ROCm.

The completion evidence is recorded in design/audits/phase-2-structural-migration.md.

Closes #7