fix: respect --engine wasm in pipeline guard (#819)

* fix: respect --engine wasm in pipeline guard

The setupPipeline function called loadNative() unconditionally, so even
with --engine wasm the Rust NativeDatabase was initialized and downstream
stages entered the native fast path. Guard the call with the engine
preference so loadNative() is skipped entirely when wasm is requested.

* fix: guard reopenNativeDb against --engine wasm (#819)

Add early return in reopenNativeDb() when engine preference is 'wasm',
making the guard self-contained rather than relying solely on callers
checking hadNativeDb. Also remove internal ticket reference from comment.

Author: carlos-alm

src/domain/graph/builder/pipeline.ts

@@ -134,7 +134,9 @@ function setupPipeline(ctx: PipelineContext): void {
   // Use NativeDatabase for schema init when native engine is available (Phase 6.13).
   // better-sqlite3 (ctx.db) is still always opened — needed for queries and stages
   // that haven't been migrated to rusqlite yet.
-  const native = loadNative();
+  // Skip native DB entirely when user explicitly requested --engine wasm.
+  const enginePref = ctx.opts.engine || 'auto';
+  const native = enginePref !== 'wasm' ? loadNative() : null;
   if (native?.NativeDatabase) {
     try {
       ctx.nativeDb = native.NativeDatabase.openReadWrite(ctx.dbPath);
@@ -216,6 +218,7 @@ function closeNativeDb(ctx: PipelineContext, label: string): void {
 
 /** Try to reopen the native connection for a given pipeline phase. */
 function reopenNativeDb(ctx: PipelineContext, label: string): void {
+  if ((ctx.opts.engine ?? 'auto') === 'wasm') return;
   const native = loadNative();
   if (!native?.NativeDatabase) return;
   try {