Minor review and refactor of vaults domain for 'polykey' #718

Specification

As part of refactoring the git domain in #298 we need to do a small review of the vaults domain for any fixes and improvements. This is a general refactor and review. We're looking for any places that can be tidied up if needed. Some tests need to be re-enabled as well.

Additional context

• Related: Review and Refactor of git/utils.ts for Serving Vault Git Repositories #298
• Related Refactoring git domain to use async generators, remove readable-stream, simplify utilities #709
• Related Adding benchmarks for git domain to polykey #717
• Related Inconsistent vault log when pulling secrets from a modified vault (received vault log is different) - should use fast forward merge #714
• Related Replace readable-stream usage with Web Streams in the Vaults and Git Domains #523

Tasks

1. General review of the vaults domain.
2. Have a closer look at the vaults committing secrets and git garbage collection code.
3. Determine and apply any optimisations that can be made.
4. Review vaults tests and clean them up if needed.
5. Re-enable any tests that have been disabled.
6. Possibly split up some test files so the vaults domain runs quicker in CI. vault ops is currently very slow.