Update project metadata, improve logging, and enhance API routes

- Change project name to "document-mcp" and update description in pyproject.toml
- Add license and keywords to pyproject.toml
- Update FastAPI server path in CLAUDE.md
- Improve error handling by replacing print statements with logging in index.py
- Remove debug print statement in mcp/server.py
- Update seed.py with a placeholder URL for mcp server
- Rename frontend package to "document-mcp-frontend" and update version and description in package.json
- Add BACKEND_AUDIT_REPORT.md to .gitignore

.gitignore

@@ -69,3 +69,4 @@ Ai-notes/
 
 # Generated reports
 AUDIT_REPORT.md
+BACKEND_AUDIT_REPORT.md

CLAUDE.md

@@ -31,7 +31,7 @@ uv pip install -e .
 uv pip install -e ".[dev]"
 
 # Run FastAPI HTTP server (for UI)
-uv run uvicorn main:app --reload --host 0.0.0.0 --port 8000
+uv run uvicorn src.api.main:app --reload --host 0.0.0.0 --port 8000
 
 # Run MCP STDIO server (for Claude Desktop/Code)
 uv run python src/mcp/server.py
@@ -76,7 +76,7 @@ npm run preview               # Serve dist/ (after npm run build)
 # Manual reset (WARNING: destroys all data)
 cd backend
 rm -f ../data/index.db
-uv run python -c "from src.services.database import DatabaseService; DatabaseService().init_schema()"
+uv run python -c "from src.services.database import DatabaseService; DatabaseService().initialize()"
 ```
 
 ## Architecture Deep Dive
@@ -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 (11 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/pyproject.toml

@@ -1,9 +1,11 @@
 [project]
-name = "Documentation-MCP"
+name = "document-mcp"
 version = "0.1.0"
-description = "Add your description here"
+description = "Multi-tenant Obsidian-like documentation viewer with AI-first workflow via MCP"
 readme = "README.md"
 requires-python = ">=3.11"
+license = {text = "MIT"}
+keywords = ["mcp", "documentation", "obsidian", "ai-agents", "fastapi", "fastmcp"]
 dependencies = [
     "fastapi>=0.121.2",
     "fastmcp>=2.13.1",

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/bigwolfe/Document-MCP/mcp",
+      "url": "https://YOUR_USERNAME-Document-MCP.hf.space/mcp",
       "headers": {
         "Authorization": "Bearer YOUR_JWT_TOKEN"
       }

frontend/package.json

@@ -1,8 +1,10 @@
 {
-  "name": "frontend",
+  "name": "document-mcp-frontend",
   "private": true,
-  "version": "0.0.0",
+  "version": "0.1.0",
   "type": "module",
+  "description": "React frontend for Document-MCP - Multi-tenant documentation viewer with AI integration",
+  "license": "MIT",
   "scripts": {
     "dev": "vite",
     "build": "tsc -b && vite build",