perf(db): migrate Repository read queries to NativeDatabase rusqlite (6.14) (#671)

* perf(db): migrate Repository read queries to NativeDatabase rusqlite (6.14)

Implement all 40 Repository read methods as Rust napi-rs methods on
NativeDatabase so every query runs via rusqlite when the native engine
is available. openRepo() now returns NativeRepository (delegating to
NativeDatabase.openReadonly) with automatic fallback to SqliteRepository.

Rust side: read_types.rs defines 14 napi return-type structs,
read_queries.rs implements 40 query methods including BFS for
getClassHierarchy and dynamic SQL for triage/fan-in queries.

TypeScript side: NativeRepository maps napi camelCase rows back to
the snake_case field names the Repository interface expects.

* fix: make line fields optional in three Native row types (#671)

The nodes table allows NULL for line, but these three Rust structs
declared line as non-optional i32. Any node with a NULL line (e.g.
file-kind nodes) would trigger a rusqlite type-mismatch error. Change
to Option<i32> in Rust and number | null in TypeScript, with ?? 0
fallback in the converter functions to match existing Repository
interface contracts.

* fix: re-throw DbError and guard ndb handle in openRepo (#671)

Re-throw DbError (e.g. DB not found) instead of silently falling back
to better-sqlite3, which would produce a misleading debug message.
Also wrap the ndb setup block in try/catch to close the handle if an
exception occurs after openReadonly, preventing resource leaks.

* fix: distinguish table-not-found from I/O errors in table checks (#671)

has_cfg_tables, has_embeddings, and has_dataflow_table previously caught
all rusqlite errors and returned false. Now only SqliteFailure (and
QueryReturnedNoRows for embeddings) map to false — genuine I/O or
connection errors propagate as napi errors.

Author: carlos-alm

crates/codegraph-core/src/lib.rs

@@ -11,6 +11,8 @@ pub mod import_resolution;
 pub mod incremental;
 pub mod insert_nodes;
 pub mod native_db;
+pub mod read_queries;
+pub mod read_types;
 pub mod parallel;
 pub mod parser_registry;
 pub mod roles_db;

crates/codegraph-core/src/native_db.rs

@@ -668,7 +668,7 @@ impl NativeDatabase {
 
 impl NativeDatabase {
     /// Get a reference to the open connection, or error if closed.
-    fn conn(&self) -> napi::Result<&Connection> {
+    pub(crate) fn conn(&self) -> napi::Result<&Connection> {
         self.conn
             .as_ref()
             .ok_or_else(|| napi::Error::from_reason("NativeDatabase is closed"))