fix: resolve Rust CI dead code and biome formatting issues

Gate test-only `NEXT_STAGE_ID` and `next_stage_id()` with `#[cfg(test)]`
in sqlite-native vfs.rs. Apply biome formatting to native.ts and
rivetkit-napi index.d.ts.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: NathanFlurry