Merge 003-chatgpt-app-integration into master - resolve conflicts

.gitignore

@@ -72,4 +72,7 @@ Ai-notes/
 *.jpg
 *.jpeg
 *.gif
+
+# Generated reports
 AUDIT_REPORT.md
+BACKEND_AUDIT_REPORT.md

CLAUDE.md

@@ -107,7 +107,7 @@ uv run python -c "from src.services.database import DatabaseService; DatabaseSer
    - `database.py`: SQLite connection manager + schema DDL
 
 3. **API/MCP** (`backend/src/api/` and `backend/src/mcp/`):
-   - `api/routes/`: FastAPI endpoints (17 routes: auth, notes CRUD, search, backlinks, tags, index health/rebuild)
+   - `api/routes/`: FastAPI endpoints (18 routes: auth, notes CRUD, search, backlinks, tags, index health/rebuild, graph, demo, system)
    - `api/middleware/auth_middleware.py`: JWT Bearer token validation
    - `mcp/server.py`: FastMCP tools (7 tools: list, read, write, delete, search, backlinks, tags)
 

backend/src/api/routes/index.py

@@ -3,9 +3,12 @@
 from __future__ import annotations
 
 from datetime import datetime
+import logging
 import time
 
 from fastapi import APIRouter, Depends, HTTPException
+
+logger = logging.getLogger(__name__)
 from pydantic import BaseModel
 
 from ...models.index import IndexHealth
@@ -120,7 +123,7 @@ async def rebuild_index(auth: AuthContext = Depends(get_auth_context)):
                 indexer_service.index_note(user_id, note_data)
                 indexed_count += 1
             except Exception as e:
-                print(f"Failed to index {note['path']}: {e}")
+                logger.error(f"Failed to index {note['path']}: {e}")
         
         # Update index health
         conn = db_service.connect()

backend/src/mcp/server.py

@@ -172,7 +172,6 @@ def read_note(
         ..., description="Relative '.md' path ≤256 chars (no '..' or '\\')."
     ),
 ) -> dict:
-    print(f"!!! READ_NOTE CALLED: {path} !!!", flush=True)
     start_time = time.time()
     user_id = _current_user_id()
 

backend/src/services/seed.py

@@ -270,7 +270,7 @@ For **HTTP mode** (HF Space), use:
 {
   "mcpServers": {
     "obsidian-docs": {
-      "url": "https://huggingface.co/spaces/YOUR_USERNAME/Document-MCP/mcp",
+      "url": "https://YOUR_USERNAME-Document-MCP.hf.space/mcp",
       "headers": {
         "Authorization": "Bearer YOUR_JWT_TOKEN"
       }