perf: native Rust build-glue queries (detect-changes, finalize, incremental)

[carlos-alm]

Summary

Move the ~46 db.prepare() calls in domain/graph/builder/stages/ (detect-changes, finalize, incremental, build-structure, collect-files) to dedicated Rust methods on NativeDatabase.

These are the "glue" queries around the native hot path — file hash checks, count queries, advisory checks. Individually cheap (1-5ms) but they add up to ~50-100ms of JS↔SQLite overhead on a full rebuild.

What to do

• Batch detect-changes hash queries into a single Rust method
• Move finalize count/advisory queries to Rust
• Move incremental hash comparison to Rust
• Goal: reduce ~46 small JS↔SQLite round-trips to 3-5 batched Rust calls

Impact

~20% of remaining native performance gap on builds. Moderate effort.