perf(db): enable auto-vacuum and add periodic maintenance

[BYK]

Issue for this PR

Closes #16729

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

Enables incremental auto-vacuum on the SQLite database and adds periodic maintenance functions.

On first run, a one-time migration checks PRAGMA auto_vacuum — if it's 0 (none), it switches to incremental mode (PRAGMA auto_vacuum = 2) and runs a full VACUUM to restructure the file. Subsequent runs skip this.

Also adds exported checkpoint() (WAL checkpoint TRUNCATE) and vacuum() (incremental vacuum 500 pages) functions for periodic maintenance.

Without auto-vacuum, the database file only grows — deleted rows leave free pages that are never reclaimed. This is especially impactful for long-running instances with session retention cleanup.

How did you verify your code works?

• Verified PRAGMA auto_vacuum switches from 0 to 2 on first run
• Confirmed checkpoint and vacuum functions execute without errors
• Tested that subsequent startups skip the migration

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR

[github-actions]

Hey! Your PR title perf(db): enable auto-vacuum and add periodic maintenance doesn't follow conventional commit format.

Please update it to start with one of:

• feat: or feat(scope): new feature
• fix: or fix(scope): bug fix
• docs: or docs(scope): documentation changes
• chore: or chore(scope): maintenance tasks
• refactor: or refactor(scope): code refactoring
• test: or test(scope): adding or updating tests

Where scope is the package name (e.g., app, desktop, opencode).

See CONTRIBUTING.md for details.