feat: migrate agents storage to v2 main database

[vaayne]

What this PR does

Before this PR:

• The v2 migration imported legacy agents data into the main SQLite database, but the runtime agents services still read and wrote the deprecated standalone agents.db database.
• Agents-only migration reruns could clear and rerun more state than necessary.

After this PR:

• Legacy agents.db content is migrated into the main v2 SQLite database through dedicated agents_* tables.
• Agents-only migration clears only the imported agents tables when re-running.
• The existing agents service layer now reads and writes the main v2 database instead of the standalone agents database.

Fixes #

Why we need it and why it was done in this way

This finishes the storage-side portion of the agents v2 migration. The data import and the runtime storage backend need to point at the same database, otherwise migrated data is not the data the application actually uses.

The following tradeoffs were made:

• The existing agents service/API surface was preserved and only its storage backend was retargeted.
• This keeps the change small and lowers regression risk, at the cost of leaving the DataApi/UI migration for a follow-up PR.

The following alternatives were considered:

• Migrate storage and renderer/API access in one PR.
• Keep the standalone agents database and defer the backend storage cutover.

Links to places where the discussion took place: None

Breaking changes

None.

Special notes for your reviewer

This PR is intentionally limited to the database migration and runtime storage cutover. The follow-up API/UI migration is split into a second PR.

Checklist

This checklist is not enforcing, but it's a reminder of items that could be relevant to every PR.
Approvers are expected to review this list.

• PR: The PR description is expressive enough and will help future contributors
• Code: Write code that humans can understand and Keep it simple
• Refactor: You have left the code cleaner than you found it (Boy Scout Rule)
• Upgrade: Impact of this change on upgrade flows was considered and addressed if required
• Documentation: A user-guide update was considered and is present (link) or not required. Check this only when the PR introduces or changes a user-facing feature or behavior.
• Self-review: I have reviewed my own code (e.g., via /gh-pr-review, gh pr diff, or GitHub UI) before requesting review from others

Release note

NONE