fix(db): chunk unresolved reference queries during sync

[msnandhis]

Summary

• chunk unresolved-reference lookups by changed file path
• chunk resolved-reference cleanup by source node id
• add regression coverage for large unresolved-reference batches
• document the fix in the unreleased changelog

Problem

Issue #540 reports codegraph sync failing on a very large checkout with too many SQL variables near the end of parsing.

getUnresolvedReferencesByFiles() built one IN (...) query containing every changed file path. Large sync batches can exceed SQLite's bind parameter limit, even though nearby node lookup code already chunks at 500 parameters for portability across SQLite backends.

deleteResolvedReferences() had the same large IN (...) shape for source node IDs, so this patch applies the same batching rule there too.

Fix

This updates both unresolved-reference paths to deduplicate inputs and process them in SQLITE_PARAM_CHUNK_SIZE chunks.

That keeps each prepared statement under the existing 500-parameter safety limit while preserving the old behavior for empty inputs and duplicate file paths or node IDs.

Closes #540.

Validation

• npx vitest run __tests__/db-perf.test.ts
• npx -y -p node@22 -p npm@10 npm run build
• npx -y -p node@22 -p npm@10 npm test
• git diff --check