feat(api): refactor database orchestration and management

[Lftobs]

Description

Please provide a summary of the changes and the motivation behind them. What problem does this PR solve?

Fixes #(issue)

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactor (no functional changes)
• CI / Build / Tooling
• Other (please describe):

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.

• Existing tests pass (bun test in apps/api/)
• New tests added (if applicable)
• Manual testing performed (describe steps)

Checklist

• My code follows the project's code style (no comments, named exports, functional components, etc.)
• I have read the contributing guidelines
• I have added tests that prove my fix is effective or that my feature works
• I have updated the documentation (if applicable)
• My changes generate no new warnings or lint errors
• I have run bun test in apps/api/ and all tests pass
• I have synced the VERSION file if needed (bun run sync-versions)

Screenshots (if applicable)

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Additional Context

Add any other context about the PR here (e.g., migration notes, deployment considerations, rollback strategy).

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