WL-0MMNCOIYF18YPLFB: add structured audit writes and doctor JSON migration apply

[SorraTheOrc]

Summary

• add a structured --audit-text write path for create/update that stores audit as { time, author, text } with generated metadata and overwrite semantics
• persist and expose audit data across DB/JSONL/API/read paths, including migration support for the audit column and show formatting updates
• fix wl doctor upgrade --confirm --json so JSON mode actually applies migrations and returns applied/backups

Validation

• npm run test -- tests/cli/issue-management.test.ts tests/cli/issue-status.test.ts tests/cli/initialization-check.test.ts tests/audit.test.ts tests/database.test.ts tests/normalize-sqlite-bindings.test.ts
• npm run test -- tests/cli/doctor-upgrade.test.ts tests/migrations.test.ts
• npm test (fails on existing unrelated tests/cli/github-push-batching.test.ts timeout/database-open issue)

Review Focus

• CLI option wiring and normalization for --audit-text in create/update paths
• persistence and migration behavior for workitems.audit
• doctor JSON-mode parity between preview and confirm paths

Work Items

• Audit Write Path via CLI Update (WL-0MMNCOIYF18YPLFB)
• Doctor upgrade --json should apply migrations with --confirm (WL-0MMZIV38S1V7XRL3)

[Copilot]

Pull request overview

Adds structured audit write support across CLI/API/DB/JSONL and fixes wl doctor upgrade --confirm --json to actually apply migrations and report results.

Changes:

• Introduces structured audit writes via --audit-text (with --audit kept as a legacy alias) and persists workitems.audit as { time, author, text }.
• Adds/updates migration and doctor-upgrade behavior to support the new audit DB column and JSON-mode apply/metadata output.
• Updates formatting/types/tests to carry audit through DB/JSONL/API/read paths.

Reviewed changes

Copilot reviewed 24 out of 24 changed files in this pull request and generated 7 comments.

Show a summary per file

File	Description
tests/unit/audit.test.ts	Removes legacy audit utility + migration tests that relied on the old audit/status model.
tests/normalize-sqlite-bindings.test.ts	Adds audit object to SQLite binding round-trip coverage.
tests/migrations.test.ts	Adds focused migration tests for adding the audit column.
tests/database.test.ts	Adds DB-level tests for creating/updating structured audit.
tests/cli/issue-status.test.ts	Verifies show --json includes audit after update --audit-text.
tests/cli/issue-management.test.ts	Adds help/CLI wiring tests for --audit-text and config gating behavior.
tests/cli/initialization-check.test.ts	Ensures update with --audit-text fails when repo is not initialized.
tests/cli/doctor-upgrade.test.ts	Adds CLI tests ensuring JSON dry-run previews and JSON confirm applies migrations.
tests/cli/cli-helpers.ts	Extends seeded work item shape to include audit in CLI tests.
tests/audit.test.ts	Adds new unit tests for buildAuditEntry under the simplified audit model.
src/types.ts	Replaces AuditEntry/status model with WorkItemAudit and adds auditWriteEnabled config.
src/tui/types.ts	Extends TUI work item type to include structured audit.
src/persistent-store.ts	Bumps schema version and includes audit column and persistence bindings.
src/migrations/index.ts	Renames/adds audit migration id and adjusts pending/apply + schemaVersion update logic.
src/jsonl.ts	Normalizes audit null/undefined during JSONL import.
src/database.ts	Ensures audit is carried through update input merging logic.
src/audit.ts	Simplifies audit entry building to { time, author, text } with author resolution.
src/commands/create.ts	Adds --audit-text option, legacy alias, and config gating for audit writes.
src/commands/update.ts	Adds --audit-text option, legacy alias, and config gating for audit writes.
src/commands/helpers.ts	Updates human formatting to display audit without the removed status field.
src/commands/doctor.ts	Makes JSON-mode doctor upgrade --confirm actually apply migrations and return applied/backups.
src/api.ts	Normalizes string audit input to structured audit and adds config gating for audit writes.
docs/migrations.md	Documents audit migration behavior and overwrite-only semantics.

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[SorraTheOrc]

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