Move memory state to a dedicated SQLite DB

[jif-oai]

Summary

Generated memory rows and their stage-one/stage-two job state currently live in state_5.sqlite alongside thread metadata. That makes memory cleanup and regeneration share the main state schema even though those rows are memory-pipeline data and can be rebuilt independently from the durable thread records.

This PR moves the memory-owned tables into a dedicated memories_1.sqlite runtime database while keeping thread metadata in state_5.sqlite.

Changes

• Adds a separate memories DB runtime, migrator, path helpers, telemetry kind, and Bazel compile data for state/memory_migrations.
• Introduces MemoryStore behind StateRuntime::memories() and moves memory table/job operations onto that store.
• Drops the old memory tables from the state DB and recreates their schema in state/memory_migrations/0001_memories.sql.
• Updates memory startup, citation usage tracking, rollout pollution handling, debug clear-memories, and app-server memory/reset to operate through the memories DB.
• Preserves cross-DB behavior by hydrating thread metadata from the state DB when selecting visible memory outputs and checking stage-one staleness.

Verification

• Added/updated codex-state tests for deleted-thread memory visibility and already-polluted phase-two enqueue behavior.
• Updated debug clear-memories, app-server memory/reset, and memories startup tests to seed and assert memory rows through memories_1.sqlite.

[jif-oai]

@codex review

[chatgpt-codex-connector]

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[jif-oai]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

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Reviewed commit: c415545cee

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

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[fcoury-oai]

Performed some basic smoke test and it worked as expected. Left one nit and one question, but none are blockers.

Approved 👍