Doctor upgrade --json should apply migrations with --confirm

[SorraTheOrc]

discovered-from:WL-0MMNCOIYF18YPLFB\n\n{
"success": true,
"pending": []
} currently returns pending migrations but does not apply them because the command returns early in JSON mode.\n\nExpected: when is provided, JSON mode should apply migrations and return applied/backups metadata, same behavior as non-JSON mode.\n\nAcceptance criteria:\n1. {
"success": true,
"pending": []
} applies pending migrations.\n2. JSON output includes applied migration IDs and backup path(s).\n3. Existing dry-run JSON behavior remains unchanged.\n4. Tests cover both JSON confirm and JSON dry-run paths.

[SorraTheOrc]

OpenCode

Implemented fix in src/commands/doctor.ts: JSON mode with --confirm now applies migrations and returns applied/backups. Dry-run JSON remains preview-only. Added regression tests in tests/cli/doctor-upgrade.test.ts for both dry-run and confirm flows. Validation passed with: npm run test -- tests/cli/doctor-upgrade.test.ts tests/migrations.test.ts.

[SorraTheOrc]

OpenCode

Committed fix: e18aace\n\nCommit message: WL-0MMZIV38S1V7XRL3: apply doctor migrations in JSON confirm mode\n\nFiles:\n- src/commands/doctor.ts\n- tests/cli/doctor-upgrade.test.ts\n\nValidation:\n- npm run test -- tests/cli/doctor-upgrade.test.ts tests/migrations.test.ts