diff --git a/gitnexus/src/config/ignore-service.ts b/gitnexus/src/config/ignore-service.ts
index affd83578f..b7fb5a3971 100644
--- a/gitnexus/src/config/ignore-service.ts
+++ b/gitnexus/src/config/ignore-service.ts
@@ -186,13 +186,65 @@ const IGNORED_FILES = new Set([
 
 
 
+// User-defined ignore patterns loaded from .gitnexusignore
+let userIgnorePatterns: string[] = [];
+let userIgnoreLoaded = false;
+
+/**
+ * Load .gitnexusignore from the repo root. Called once per analysis.
+ * Format: one pattern per line, # comments, blank lines ignored.
+ * Patterns are path prefixes (e.g., "app/engine/source/") or
+ * directory names (e.g., "workspace") matched against path segments.
+ */
+export const loadIgnoreFile = async (repoPath: string): Promise<void> => {
+  if (userIgnoreLoaded) return;
+  userIgnoreLoaded = true;
+
+  const fs = await import('fs/promises');
+  const path = await import('path');
+  const ignorePath = path.join(repoPath, '.gitnexusignore');
+
+  try {
+    const content = await fs.readFile(ignorePath, 'utf-8');
+    userIgnorePatterns = content
+      .split('\n')
+      .map(line => line.trim())
+      .filter(line => line.length > 0 && !line.startsWith('#'));
+  } catch {
+    // No .gitnexusignore file — that's fine
+    userIgnorePatterns = [];
+  }
+};
+
+/** Reset loaded state (for testing or re-indexing) */
+export const resetIgnoreFile = (): void => {
+  userIgnorePatterns = [];
+  userIgnoreLoaded = false;
+};
+
 export const shouldIgnorePath = (filePath: string): boolean => {
   const normalizedPath = filePath.replace(/\\/g, '/');
   const parts = normalizedPath.split('/');
   const fileName = parts[parts.length - 1];
   const fileNameLower = fileName.toLowerCase();
 
-  // Check if any path segment is in ignore list
+  // Check user-defined .gitnexusignore patterns first
+  for (const pattern of userIgnorePatterns) {
+    // Path prefix match: "app/engine/source/" matches "app/engine/source/foo.ts"
+    if (pattern.includes('/')) {
+      const cleanPattern = pattern.replace(/\/+$/, '');
+      if (normalizedPath.startsWith(cleanPattern + '/') || normalizedPath === cleanPattern) {
+        return true;
+      }
+    } else {
+      // Directory name match: "workspace" matches any path segment
+      if (parts.includes(pattern)) {
+        return true;
+      }
+    }
+  }
+
+  // Check if any path segment is in default ignore list
   for (const part of parts) {
     if (DEFAULT_IGNORE_LIST.has(part)) {
       return true;
diff --git a/gitnexus/src/core/ingestion/filesystem-walker.ts b/gitnexus/src/core/ingestion/filesystem-walker.ts
index 7074593a0a..82845352c6 100644
--- a/gitnexus/src/core/ingestion/filesystem-walker.ts
+++ b/gitnexus/src/core/ingestion/filesystem-walker.ts
@@ -1,7 +1,7 @@
 import fs from 'fs/promises';
 import path from 'path';
 import { glob } from 'glob';
-import { shouldIgnorePath } from '../../config/ignore-service.js';
+import { shouldIgnorePath, loadIgnoreFile } from '../../config/ignore-service.js';
 
 export interface FileEntry {
   path: string;
@@ -32,6 +32,9 @@ export const walkRepositoryPaths = async (
   repoPath: string,
   onProgress?: (current: number, total: number, filePath: string) => void
 ): Promise<ScannedFile[]> => {
+  // Load .gitnexusignore before filtering
+  await loadIgnoreFile(repoPath);
+
   const files = await glob('**/*', {
     cwd: repoPath,
     nodir: true,