Move SQLite persistence to Effect SQL and Drizzle

[alandotcom]

Replace production node:sqlite repository access with drizzle-orm/effect-sqlite-node while preserving wfSqlite(), stored data, repository contracts, and transaction behavior. This moves connection lifecycle and serialized BEGIN IMMEDIATE writes into Effect SQL and makes generated Drizzle migrations the schema source of truth.

Review guide

Start with packages/core/src/backend/persistence/sqlite/migrations.ts and database.ts, then the generated schema and migration tests. The main risk surfaces are legacy database adoption, rollback under failed migrations, and the installed-package path for the patched Drizzle adapter.

What changed

• Adopt exact version 6 and 7 SQLite schemas into __wfgraph_sqlite_migrations without rewriting application tables. Reject older, partial, altered, tampered, or newer schemas instead of guessing.
• Run migration inspection, adoption, journal validation, generated SQL, foreign-key checks, and final fingerprint validation in one transaction.
• Convert SQLite repositories to Effect-native Drizzle SQL while retaining payload-safe DatabaseError translation and existing row contracts.
• Add a generated SQLite baseline and validation script.
• Patch Drizzle RC4 for Effect RC112 compatibility and bundle the adapter so published consumers do not need the pnpm patch. The upstream fix is rc.5 drizzle-team/drizzle-orm#5966.
• Pack and install @wfgraph/core in a clean directory during PR checks, then open and migrate SQLite through the published entry.

Validation

• pnpm install --frozen-lockfile
• pnpm run check
• pnpm run type-check
• pnpm run lint
• pnpm run test: 3,289 passed; 37 PostgreSQL tests skipped in the general suite
• WFGRAPH_REQUIRE_POSTGRES=1 WFGRAPH_TEST_DATABASE_URL=... pnpm run test:postgres: 37 passed
• pnpm run build
• pnpm run knip
• pnpm run skills:validate
• pnpm run db:generate:sqlite
• pnpm run package:smoke

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-02T00:43:58.960567Z	239b3c3	New commits
🔒 Security Review	✅ Completed 2026-09-01T23:59:09.947034Z	c70ca83	PR opened

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commit: 239b3c3