feat(cli): add system onnxruntime-node binding override

gitnexus/README.md

@@ -192,6 +192,15 @@ gitnexus analyze . --embeddings
 
 Works with Infinity, vLLM, TEI, llama.cpp, Ollama, LM Studio, or OpenAI. When unset, local embeddings are used unchanged.
 
+## System ONNX Runtime Binding (Advanced)
+
+If your environment provides a system-built onnxruntime-node binding (for example, Nix),
+you can direct GitNexus to use it instead of the package's bundled binary:
+
+```bash
+export GITNEXUS_ORT_BINDING_PATH=/absolute/path/to/onnxruntime_binding.node
+```
+
 ## Multi-Repo Support
 
 GitNexus supports indexing multiple repositories. Each `gitnexus analyze` registers the repo in a global registry (`~/.gitnexus/registry.json`). The MCP server serves all indexed repos automatically.

gitnexus/src/core/embeddings/embedder.ts

@@ -28,6 +28,7 @@ import { DEFAULT_EMBEDDING_CONFIG, type EmbeddingConfig, type ModelProgress } fr
 import { isHttpMode, getHttpDimensions, httpEmbed } from './http-client.js';
 import { resolveEmbeddingConfig } from './config.js';
 import { applyHfEnvOverrides, isHfDownloadFailure, withHfDownloadRetry } from './hf-env.js';
+import { applyOnnxruntimeNodeBindingOverride } from './onnxruntime-node-loader.js';
 import { logger } from '../logger.js';
 
 /**
@@ -164,6 +165,7 @@ export const initEmbedder = async (
     try {
       // Configure transformers.js environment
       env.allowLocalModels = false;
+      applyOnnxruntimeNodeBindingOverride();
       // Bridge user-controlled env vars to transformers.js: HF_HOME →
       // env.cacheDir, HF_ENDPOINT → env.remoteHost (#1205). Centralised in
       // applyHfEnvOverrides so the MCP embedder entry point behaves

gitnexus/src/core/embeddings/onnxruntime-node-loader.ts

@@ -0,0 +1,53 @@
+import Module from 'module';
+import { existsSync } from 'fs';
+import { isAbsolute } from 'path';
+
+const OVERRIDE_ENV = 'GITNEXUS_ORT_BINDING_PATH';
+
+/**
+ * Redirect onnxruntime-node to a system-provided binding binary.
+ *
+ * onnxruntime-node always requires a native .node file from its own package.
+ * We patch Node's module resolver so that specific request is redirected to
+ * the path provided by GITNEXUS_ORT_BINDING_PATH.
+ */
+export const applyOnnxruntimeNodeBindingOverride = (): void => {
+  const overridePath = process.env[OVERRIDE_ENV];
+  if (!overridePath) return;
+
+  if (!isAbsolute(overridePath)) {
+    throw new Error(`${OVERRIDE_ENV} must be an absolute path, got "${overridePath}"`);
+  }
+
+  if (!existsSync(overridePath)) {
+    throw new Error(`${OVERRIDE_ENV} points to a missing file: "${overridePath}"`);
+  }
+
+  const moduleAny = Module as typeof Module & {
+    _gitnexusOrtBindingOverrideApplied?: boolean;
+    _resolveFilename?: (
+      request: string,
+      parent: NodeModule | null,
+      isMain: boolean,
+      options?: unknown
+    ) => string;
+  };
+
+  if (moduleAny._gitnexusOrtBindingOverrideApplied) return;
+  moduleAny._gitnexusOrtBindingOverrideApplied = true;
+
+  const originalResolve = moduleAny._resolveFilename?.bind(Module);
+  if (!originalResolve) return;
+
+  moduleAny._resolveFilename = function (
+    request: string,
+    parent: NodeModule | null,
+    isMain: boolean,
+    options?: unknown
+  ): string {
+    if (typeof request === 'string' && request.endsWith('onnxruntime_binding.node')) {
+      return overridePath;
+    }
+    return originalResolve(request, parent, isMain, options);
+  };
+};

gitnexus/src/mcp/core/embedder.ts

@@ -17,6 +17,7 @@ import {
   isHfDownloadFailure,
   withHfDownloadRetry,
 } from '../../core/embeddings/hf-env.js';
+import { applyOnnxruntimeNodeBindingOverride } from '../../core/embeddings/onnxruntime-node-loader.js';
 import { silenceStdout, restoreStdout, realStderrWrite } from '../../core/lbug/pool-adapter.js';
 
 import { logger } from '../../core/logger.js';
@@ -49,6 +50,7 @@ export const initEmbedder = async (): Promise<FeatureExtractionPipeline> => {
   initPromise = (async () => {
     try {
       env.allowLocalModels = false;
+      applyOnnxruntimeNodeBindingOverride();
       // Bridge user-controlled env vars to transformers.js: HF_HOME →
       // env.cacheDir, HF_ENDPOINT → env.remoteHost (#1205). Centralised in
       // applyHfEnvOverrides so this MCP entry point behaves identically to