fix(native): exclude prototype patterns from WASM post-pass pre-filter

The regex /\b\w+\.\w+\s*=\s*function/ matched the substring
'prototype.bar = function' inside 'Foo.prototype.bar = function(){}',
causing prototype files to be queued for WASM re-processing even though
the Rust engine now handles those patterns natively. Added a negative
lookahead to exclude the prototype shape, matching only
function-as-object-property patterns like 'fn.method = function'.

Fixes the duplicate-node risk flagged in Greptile review of #1339.

Author: carlos-alm

src/domain/graph/builder/stages/native-orchestrator.ts

@@ -598,7 +598,7 @@ async function runPostNativePrototypeMethods(
   const protoFiles = jsFiles.filter((relPath) => {
     try {
       const content = readFileSafe(path.join(rootDir, relPath));
-      return /\b\w+\.\w+\s*=\s*function/.test(content);
+      return /\b(?!prototype\.)\w+\.\w+\s*=\s*function/.test(content);
     } catch {
       return false;
     }