[codex] Refactor note and journal canonical metadata

[h4yfans]

What

Move note and journal canonical metadata into data.db, add storage/domain packages around it, and rewire vault, IPC, watcher, and sync flows to treat index.db as a rebuildable projection instead of the source of truth.

Why

This architecture-reset slice needs note and journal metadata to survive index rebuilds and stop depending on note_cache in index.db for canonical state. Property definitions also need to live with the canonical note metadata rather than only in the rebuildable index.

How

• add note_metadata and canonical property_definitions tables to data.db
• add @memry/storage-data, @memry/storage-vault, and @memry/domain-notes packages
• route note/journal indexing, vault mutations, IPC handlers, watcher delete/rename flows, and sync handlers through canonical metadata in data.db
• keep index.db as the search/projection cache and mirror only the rebuildable note cache state there
• update migrations, generated IPC invoke map, lockfile, and tests for the new note/journal boundary

Type

• feat — new feature
• fix — bug fix
• refactor — restructure without behavior change
• style — visual/UI only
• perf — performance improvement
• test — adding or updating tests
• chore — tooling, deps, config
• docs — documentation only
• ci — CI/CD changes

Test plan

• Unit tests added/updated
• Integration tests added/updated
• Manual testing (describe below)

Validation run:

• pnpm --filter @memry/db-schema typecheck
• pnpm --filter @memry/domain-notes typecheck
• pnpm --filter @memry/storage-data typecheck
• pnpm --filter @memry/storage-vault typecheck
• pnpm --filter @memry/desktop typecheck
• pnpm --filter @memry/desktop exec vitest run --config config/vitest.config.ts --project main src/main/ipc/journal-handlers.test.ts src/main/vault/indexer.test.ts src/main/vault/watcher.test.ts src/main/vault/note-sync.test.ts src/main/database/migrate.test.ts src/main/sync/item-handlers/note-handler-binary.test.ts
• pnpm --filter @memry/desktop exec vitest run --config config/vitest.config.ts --project shared ../../packages/domain-notes/src/commands.test.ts ../../packages/db-schema/src/data-schema.test.ts

Checklist

• Self-reviewed the diff
• No hardcoded secrets or credentials
• Files stay under ~500 LOC
• Follows immutable data patterns