kernel: real SqliteMetadataStore — SQLAlchemy models for all entities + initial migration

[JArmandoAnaya]

Replaces the bootstrap stub (engine + empty MetaData) with the persistence floor every M1 service sits on.

What landed

• Tables for all fourteen entities (adapters/_tables.py, private) — flat columns where the model is flat; child tables for batch_asset and annotation_job_asset; JSON for the immutable nested values (annotation_schema.classes, annotation.geometry, release.manifest).
• Mapping layer (adapters/_mappers.py, private) — one EntityMapping per entity, so no SQLAlchemy type reaches a domain or port signature. adapters/__init__ still exports only SqliteMetadataStore.
• Port — a generic Repository[T] plus a UnitOfWork, instead of ~50 per-entity methods. Every child entity has exactly one parent FK, so list(parent_id=...) covers every scoped read.
• Migration 001 (adapters/migrations.py) — an ordered MIGRATIONS list with FORMAT_VERSION derived from it. initialize() runs what is missing and refuses a workspace stamped ahead of this build.
• Unit of work — with store.unit_of_work() as uow: commits on clean exit, rolls back on any exception.
• kernel/errors.py — VisionSetError and the three errors this layer raises.
• DatasetMember / DatasetChange domain models (shapes only; the rules are kernel: DatasetService — promotion from completed batches, mutation change log #11's).
• docs/persistence.md.

Decisions

• Hand-rolled versioned DDL, not alembic. A local-first single-file store does not need a migration framework, and format_version would then duplicate alembic_version.
• classes/geometry/manifest as JSON, membership/progress as child tables — immutable values that rehydrate whole vs. relations edited one row at a time.
• Timestamps are TEXT holding ISO-8601 with offset. SQLite's DATETIME storage drops the timezone; naive datetimes are rejected at construction.
• PRAGMA foreign_keys = ON per connection — SQLite ships with foreign keys off, so every FK here would otherwise be decorative. There is a test that fails without the listener.

Scope: persistence only. No services, no state machines, no name-uniqueness rules — those are #4–#12.

Gates

Gate	Result
uv run pytest	65 passed
uv run ruff check . / ruff format --check .	clean, 60 files formatted
uv run mypy src/visionset/kernel	no issues, 31 files
uv run mypy src/visionset	no issues, 41 files
uv run lint-imports	2 contracts kept, 0 broken
scripts/export_openapi.py	no drift

Closes #3