diff --git a/apps/backend/spec/complexity.py b/apps/backend/spec/complexity.py
index 9a1770a0..6d4e8282 100644
--- a/apps/backend/spec/complexity.py
+++ b/apps/backend/spec/complexity.py
@@ -382,7 +382,7 @@ async def run_ai_complexity_assessment(
         context += f"\n**Task Description**: {task_description or 'Not provided'}\n"
 
     # Add project index if available
-    auto_build_index = spec_dir.parent.parent / "auto-claude" / "project_index.json"
+    auto_build_index = spec_dir.parent.parent / "project_index.json"
     if auto_build_index.exists():
         context += f"\n**Project Index**: Available at {auto_build_index}\n"
 
diff --git a/apps/backend/spec/context.py b/apps/backend/spec/context.py
index 61771999..4d06d0a4 100644
--- a/apps/backend/spec/context.py
+++ b/apps/backend/spec/context.py
@@ -34,7 +34,7 @@ def run_context_discovery(
     if context_file.exists():
         return True, "context.json already exists"
 
-    script_path = project_dir / "auto-claude" / "context.py"
+    script_path = project_dir / ".auto-claude" / "context.py"
     if not script_path.exists():
         return False, f"Script not found: {script_path}"
 
diff --git a/apps/backend/spec/discovery.py b/apps/backend/spec/discovery.py
index e2254eb0..159ac477 100644
--- a/apps/backend/spec/discovery.py
+++ b/apps/backend/spec/discovery.py
@@ -24,7 +24,7 @@ def run_discovery_script(
         (success, output_message)
     """
     spec_index = spec_dir / "project_index.json"
-    auto_build_index = project_dir / "auto-claude" / "project_index.json"
+    auto_build_index = project_dir / ".auto-claude" / "project_index.json"
 
     # Check if project_index already exists
     if auto_build_index.exists() and not spec_index.exists():
diff --git a/apps/backend/spec/phases/utils.py b/apps/backend/spec/phases/utils.py
index 704b6bee..b9306fcf 100644
--- a/apps/backend/spec/phases/utils.py
+++ b/apps/backend/spec/phases/utils.py
@@ -22,7 +22,7 @@ def run_script(project_dir: Path, script: str, args: list[str]) -> tuple[bool, s
     Returns:
         Tuple of (success: bool, output: str)
     """
-    script_path = project_dir / "auto-claude" / script
+    script_path = project_dir / ".auto-claude" / script
 
     if not script_path.exists():
         return False, f"Script not found: {script_path}"
diff --git a/apps/backend/spec/pipeline/orchestrator.py b/apps/backend/spec/pipeline/orchestrator.py
index 0654a7fd..5f3ba923 100644
--- a/apps/backend/spec/pipeline/orchestrator.py
+++ b/apps/backend/spec/pipeline/orchestrator.py
@@ -603,7 +603,7 @@ class SpecOrchestrator:
             The complexity assessment
         """
         project_index = {}
-        auto_build_index = self.project_dir / "auto-claude" / "project_index.json"
+        auto_build_index = self.project_dir / ".auto-claude" / "project_index.json"
         if auto_build_index.exists():
             with open(auto_build_index, encoding="utf-8") as f:
                 project_index = json.load(f)