feat(server): let t3.json limit or disable submodule init in new worktrees - #12953

Eligibility
This adds a small, opt-in t3.json setting for recursive, top-level, or disabled submodule initialization while preserving the existing recursive default. The new modes are covered by integration and schema tests, with no breaking or sensitive-surface changes.

Notes:
No code owners found in target merge base e1cbb70