chore(db): drop retired storage whose readers have shipped

[waleedlatif1]

Summary

• Drops retired storage whose last readers/writers were removed in already-released versions: organization_search_invocation (chore(search): remove legacy indexed enterprise search #8528, v0.9.10), copilot_task_subscriptions (never used by a released Sim or worker version), copilot_workflow_read_hashes (improvement(mothership): restructured stream, tool structures, code typing, file write/patch/append tools, timing issues #4090, v0.6.40), mothership_settings (improvement(mothership): v0.2 #4923, v0.7.0), academy_certificate + academy_cert_status (fix(seo): fix GSC indexing issues, remove unused academy/partners pages #5388, v0.7.22), and doc_processing_recovery_idx (superseded by the per-connector recovery index in improvement(knowledge): scan processing recovery per connector and prune finished outbox events #8330, v0.9.4)
• Drops embedding_keyword_tin (fix(db): retire unused keyword search projections #8810, v0.9.17) in script migration 0031, not SQL — SQL runs before scripts, so an upgrade that skips 0030's release would otherwise drop the table under its still-installed writer triggers. 0030 now tolerates the table being gone (db:push drops it before the reconciler runs)
• chat.include_tool_calls → NOT NULL DEFAULT false (closes its contract-pending(any release) marker). Default, backfill, and SET NOT NULL run under one NOWAIT lock on chat so a fork copying a legacy null row can't land in between; removed the now-dead ?? false handling in the chat routes/presenters
• Un-declares dead columns copilot_chats.plan_artifact, copilot_messages.parent_message_id/tokens_in/tokens_out, settings.show_training_controls/copilot_enabled_models — v0.9.18's generated inserts still name them, so their DROP COLUMN is owed next release (contract-pending markers on each table)
• Table drops autocommit one by one with a 100ms lock timeout so FK-parent locks (user, workspace, workflow, ...) fail fast and retry instead of piling up in one transaction

Left alone on purpose: project membership tables (#8590), legacy file-search index tables (#8014), embedding_search ACL/binary columns and knowledge_projection_dirty (still written by DB triggers).

Type of Change

• Chore / maintenance

Testing

• Verified every dropped/un-declared name has no references at HEAD, at v0.9.18 / v0.9.17, in the worker repo, or in DB triggers/functions
• check:migrations, check:pending-drop-tables, check:schema-mock, check:comment-hygiene, check:test-patterns, block-registry check, bun run lint; drizzle-kit generate is a no-op
• Type-check packages/db + packages/testing; chat route/deployment + data-drain tests (23 files, 167 tests)
• New 0030 integration test covers retiring the writers after Tin is already dropped; fresh migrate/push provisioning in CI exercises 0409 + 0031

Checklist

• Code follows project style guidelines
• Self-reviewed my changes
• Tests added/updated and passing (new tests pass the test-audit authoring gate)
• No new warnings introduced
• I confirm that I have read and agree to the terms outlined in the Contributor License Agreement (CLA)

[cubic-dev-ai]

No issues found across 24 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

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[greptile-apps]

Confidence Score: 5/5

[Critical impact] The PR appears safe to merge; the previous chat-lock issue is fixed and no new actionable issues were found.

Summary

Removes retired storage, makes chat.include_tool_calls required with a default of false, and updates callers and tests.

• Database migrations remove storage that no released code uses.
• Database upgrades stop keyword writers before dropping Tin.
• Chat deployments store tool-call settings as true or false.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[SQL migrations] --> B[0409 removes retired storage]
  B --> C[0030 retires keyword writers]
  C --> D[0031 drops keyword Tin]

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_{Reviews (2) · Last reviewed commit: "fix(db): bound the chat lock in 0409 wit..." · Reviewed by Greptile}

[waleedlatif1]

@greptile

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Project	Deployment	Actions	Updated
docs	Ready	Preview	Oct 12, 2026 7:52pm UTC

[waleedlatif1]

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[cubic-dev-ai]

@cubic-dev-ai review this PR

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[cubic-dev-ai]

No issues found across 24 files

Confidence score: 5/5

• Automated review surfaced no issues in the provided summaries.
• No files require special attention.

<sub>Heads up: you’ve reached your flex budget. Increase your flex budget or wait for usage to reset.

Turn on auto-fix | Re-trigger cubic</sub>