Update README

chore(deps): update docker.io/library/python:3.12-slim-trixie docker digest to b43ff04

.github/workflows/bump-version.yml

@@ -15,7 +15,7 @@ jobs:
       packages: write
     steps:
       - name: Check out
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
           token: "${{ secrets.PERSONAL_ACCESS_TOKEN }}"

.github/workflows/docker-build-publish.yml

@@ -12,7 +12,7 @@ jobs:
       packages: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
 
       - name: Docker meta
         id: meta

.github/workflows/helm-release.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
         with:
           fetch-depth: 0
 

.github/workflows/release.yml

@@ -18,9 +18,9 @@ jobs:
       contents: read
     steps:
       - name: Checkout
-        uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
+        uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
       - name: Install uv
-        uses: astral-sh/setup-uv@5a7eac68fb9809dea845d802897dc5c723910fa3 # v7.1.3
+        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
       - name: Install Python 3.11
         run: uv python install 3.11
       - name: Build

.github/workflows/test.yml

@@ -9,9 +9,9 @@ jobs:
   linting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5.0.1
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@5a7eac68fb9809dea845d802897dc5c723910fa3 # v7.1.3
+        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
       - name: Check format
         run: |
           uv run --frozen ruff format --diff
@@ -27,7 +27,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5.0.1
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
         with:
           submodules: 'true'
 
@@ -56,7 +56,7 @@ jobs:
           up-flags: "--build"
 
       - name: Install the latest version of uv
-        uses: astral-sh/setup-uv@5a7eac68fb9809dea845d802897dc5c723910fa3 # v7.1.3
+        uses: astral-sh/setup-uv@1e862dfacbd1d6d858c55d9b792c756523627244 # v7.1.4
 
       - name: Install Playwright dependencies
         run: |

CHANGELOG.md

@@ -1,3 +1,67 @@
+## v0.46.2 (2025-11-22)
+
+### Fix
+
+- **smithery**: Enable JSON response format for scanner compatibility
+
+## v0.46.1 (2025-11-22)
+
+### Perf
+
+- Optimize vector viz search performance
+
+## v0.46.0 (2025-11-22)
+
+### Feat
+
+- Add Smithery CLI deployment support
+- Implement ADR-016 Smithery stateless deployment mode
+
+### Fix
+
+- **smithery**: Add JSON Schema metadata to mcp-config endpoint
+- **smithery**: Use container runtime pattern for config discovery
+- Add Smithery lifespan and auth mode detection
+
+## v0.45.0 (2025-11-22)
+
+### Feat
+
+- Add context expansion to semantic search with chunk overlap removal
+- Use Ollama native batch API in embed_batch()
+- Implement Qdrant placeholder state management
+- Switch files to use numeric IDs with file_path resolution
+- Implement per-chunk vector visualization with context expansion
+
+### Fix
+
+- Use alpha_composite for proper RGBA highlight blending
+- Remove pymupdf.layout.activate() to fix page_chunks behavior
+- Centralize PDF processing and generate separate images per chunk
+- Set is_placeholder=False in processor to fix search filtering
+- Increase placeholder staleness threshold to 5x scan interval
+- Add placeholder staleness check to prevent duplicate processing
+- Use empty SparseVector instead of None for placeholders
+- Return empty array instead of null for query_coords when no results
+- Align PDF text extraction between indexing and context expansion
+- Update models and viz to use int-only doc_id
+- Reconstruct full content for notes to match indexed offsets
+- Add async/await, PDF metadata, and type safety fixes
+
+### Refactor
+
+- Simplify PDF text extraction with single to_markdown call
+
+### Perf
+
+- Optimize PDF processing with parallel extraction and single-render highlights
+
+## v0.44.1 (2025-11-21)
+
+### Fix
+
+- **deps**: update dependency mcp to >=1.22,<1.23
+
 ## v0.44.0 (2025-11-19)
 
 ### Feat

Dockerfile

@@ -1,12 +1,13 @@
-FROM docker.io/library/python:3.12-slim-trixie@sha256:2e683fc3e18a248aa23b8022f2a3474b072b04fb851efe9b49f6b516a8944939
+FROM docker.io/library/python:3.12-slim-trixie@sha256:b43ff04d5df04ad5cabb80890b7ef74e8410e3395b19af970dcd52d7a4bff921
 
-COPY --from=ghcr.io/astral-sh/uv:0.9.10@sha256:29bd45092ea8902c0bbb7f0a338f0494a382b1f4b18355df5be270ade679ff1d /uv /uvx /bin/
+COPY --from=ghcr.io/astral-sh/uv:0.9.11@sha256:5aa820129de0a600924f166aec9cb51613b15b68f1dcd2a02f31a500d2ede568 /uv /uvx /bin/
 
 # Install dependencies
 # 1. git (required for caldav dependency from git)
 # 2. sqlite for development with token db
 RUN apt update && apt install --no-install-recommends --no-install-suggests -y \
     git \
+    tesseract-ocr \
     sqlite3 && apt clean
 
 WORKDIR /app
@@ -17,5 +18,7 @@ RUN uv sync --locked --no-dev --no-editable --no-cache
 
 ENV PYTHONUNBUFFERED=1
 ENV VIRTUAL_ENV=/app/.venv
+ENV PATH=/app/.vnev/bin:$PATH
+ENV TESSDATA_PREFIX=/usr/share/tesseract-ocr/5/tessdata
 
 ENTRYPOINT ["/app/.venv/bin/nextcloud-mcp-server", "--host", "0.0.0.0"]

Dockerfile.smithery

@@ -0,0 +1,44 @@
+# Dockerfile for Smithery stateless deployment
+# ADR-016: Stateless mode for multi-user public Nextcloud instances
+#
+# This image excludes:
+# - Vector database dependencies (qdrant-client)
+# - Background sync workers
+# - Admin UI routes (/app)
+# - Semantic search tools
+#
+# Features included:
+# - Core Nextcloud tools (notes, calendar, contacts, files, deck, tables, cookbook)
+# - Per-session app password authentication
+# - Multi-user support via Smithery session config
+
+FROM docker.io/library/python:3.12-slim-trixie@sha256:b43ff04d5df04ad5cabb80890b7ef74e8410e3395b19af970dcd52d7a4bff921
+
+WORKDIR /app
+
+# Install uv for fast dependency management
+COPY --from=ghcr.io/astral-sh/uv:0.9.11@sha256:5aa820129de0a600924f166aec9cb51613b15b68f1dcd2a02f31a500d2ede568 /uv /uvx /bin/
+
+# Install dependencies
+# 1. git (required for caldav dependency from git)
+# 2. sqlite for development with token db
+RUN apt update && apt install --no-install-recommends --no-install-suggests -y \
+    git
+
+# Copy project files
+COPY . .
+
+RUN uv sync --locked --no-dev --no-editable --no-cache
+
+# Set Smithery mode environment variables
+ENV SMITHERY_DEPLOYMENT=true
+ENV VECTOR_SYNC_ENABLED=false
+
+# Smithery sets PORT=8081 by default
+EXPOSE 8081
+
+# Health check endpoint
+HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
+    CMD uv run python -c "import httpx; httpx.get('http://localhost:${PORT:-8081}/health/live').raise_for_status()"
+
+CMD ["/app/.venv/bin/smithery-main"]

README.md

@@ -1,9 +1,11 @@
+```markdown
 <p align="center">
   <img src="astrolabe.svg" alt="Nextcloud MCP Server" width="128" height="128">
 </p>
 
 # Nextcloud MCP Server
 
+[![smithery badge](https://smithery.ai/badge/@cbcoutinho/nextcloud-mcp-server)](https://smithery.ai/server/@cbcoutinho/nextcloud-mcp-server)
 [![Docker Image](https://img.shields.io/badge/docker-ghcr.io/cbcoutinho/nextcloud--mcp--server-blue)](https://github.com/cbcoutinho/nextcloud-mcp-server/pkgs/container/nextcloud-mcp-server)
 
 **A production-ready MCP server that connects AI assistants to your Nextcloud instance.**
@@ -17,7 +19,20 @@ This is a **dedicated standalone MCP server** designed for external MCP clients
 
 ## Quick Start
 
-Get up and running in 60 seconds using Docker:
+The fastest way to get started is via [Smithery](https://smithery.ai/server/@cbcoutinho/nextcloud-mcp-server) - no Docker or self-hosting required:
+
+1. Visit the [Smithery marketplace page](https://smithery.ai/server/@cbcoutinho/nextcloud-mcp-server)
+2. Click "Deploy" and configure:
+   - **Nextcloud URL**: Your Nextcloud instance (e.g., `https://cloud.example.com`)
+   - **Username**: Your Nextcloud username
+   - **App Password**: Generate one in Nextcloud → Settings → Security → Devices & sessions
+
+> [!NOTE]
+> Smithery runs in stateless mode without semantic search. For full features, use [Docker](#docker-self-hosted) or see [ADR-016](docs/ADR-016-smithery-stateless-deployment.md).
+
+## Docker (Self-Hosted)
+
+For full features including semantic search, run with Docker:
 
 ```bash
 # 1. Create a minimal configuration
@@ -37,12 +52,11 @@ curl http://127.0.0.1:8000/health/ready
 # 4. Connect to the endpoint
 http://127.0.0.1:8000/sse
 
-# 4. Or with --transport streamable-http
+# Or with --transport streamable-http
 http://127.0.0.1:8000/mcp
 ```
 
 **Next Steps:**
-- Create an app password in Nextcloud: Settings → Security → Devices & sessions
 - Connect your MCP client (Claude Desktop, IDEs, `mcp dev`, etc.)
 - See [docs/installation.md](docs/installation.md) for other deployment options (local, Kubernetes)
 
@@ -210,3 +224,4 @@ This project is licensed under the AGPL-3.0 License. See [LICENSE](./LICENSE) fo
 - [Model Context Protocol](https://github.com/modelcontextprotocol)
 - [MCP Python SDK](https://github.com/modelcontextprotocol/python-sdk)
 - [Nextcloud](https://nextcloud.com/)
+```

charts/nextcloud-mcp-server/Chart.lock

@@ -4,6 +4,6 @@ dependencies:
   version: 1.16.0
 - name: ollama
   repository: https://otwld.github.io/ollama-helm
-  version: 1.34.0
-digest: sha256:9dfb8d6e3d5488f669d4c37f3a766213b598ff3de2aead2c734789736c7835b4
-generated: "2025-11-17T17:08:48.055530019Z"
+  version: 1.35.0
+digest: sha256:da8db198b12ce0252df220fabb297cfe69186edb8e67952c52e05de778189b92
+generated: "2025-11-21T11:09:07.997781541Z"

charts/nextcloud-mcp-server/Chart.yaml

@@ -2,8 +2,8 @@ apiVersion: v2
 name: nextcloud-mcp-server
 description: A Helm chart for Nextcloud MCP Server - enables AI assistants to interact with Nextcloud
 type: application
-version: 0.44.0
-appVersion: "0.44.0"
+version: 0.46.2
+appVersion: "0.46.2"
 keywords:
   - nextcloud
   - mcp
@@ -31,6 +31,6 @@ dependencies:
     repository: https://qdrant.github.io/qdrant-helm
     condition: qdrant.networkMode.deploySubchart
   - name: ollama
-    version: "1.34.0"
+    version: "1.35.0"
     repository: https://otwld.github.io/ollama-helm
     condition: ollama.enabled

docker-compose.yml

@@ -17,11 +17,11 @@ services:
   # Note: Redis is an external service. You can find more information about the configuration here:
   # https://hub.docker.com/_/redis
   redis:
-    image: docker.io/library/redis:alpine@sha256:5013e94192ef18a5d8368179c7522e5300f9265cc339cadac76c7b93303a2752
+    image: docker.io/library/redis:alpine@sha256:6cbef353e480a8a6e7f10ec545f13d7d3fa85a212cdcc5ffaf5a1c818b9d3798
     restart: always
 
   app:
-    image: docker.io/library/nextcloud:32.0.1@sha256:d572839eeb693026d72a0c6aa48076df0bb8930797ea321e604936ef7189d06e
+    image: docker.io/library/nextcloud:32.0.2@sha256:ac08482d73ffd85d94069ba291bbd5fb39a70ff21502030a2e3e2d89a7246a48
     restart: always
     ports:
       - 0.0.0.0:8080:80
@@ -224,6 +224,26 @@ services:
       - keycloak-tokens:/app/data
       - keycloak-oauth-storage:/app/.oauth
 
+  # Smithery stateless deployment mode (ADR-016)
+  # Test with: docker compose --profile smithery up smithery
+  # Then: curl http://localhost:8081/.well-known/mcp-config
+  smithery:
+    build:
+      context: .
+      dockerfile: Dockerfile.smithery
+    restart: always
+    depends_on:
+      app:
+        condition: service_healthy
+    ports:
+      - 127.0.0.1:8081:8081
+    environment:
+      - SMITHERY_DEPLOYMENT=true
+      - VECTOR_SYNC_ENABLED=false
+      - PORT=8081
+    profiles:
+      - smithery
+
   qdrant:
     image: qdrant/qdrant:v1.16.0@sha256:1005201498cf927d835383d0f918b17d8c9da7db58550f169f694455e42d78f4
     restart: always

docs/ADR-016-smithery-stateless-deployment.md

@@ -0,0 +1,492 @@
+# ADR-016: Smithery Stateless Deployment for Multi-User Public Nextcloud Instances
+
+**Status:** Proposed
+**Date:** 2025-01-22
+**Deciders:** Development Team
+**Related:** ADR-004 (OAuth), ADR-007 (Background Vector Sync), ADR-015 (Unified Provider)
+
+## Context
+
+[Smithery](https://smithery.ai) is a hosting platform and marketplace for MCP servers that provides:
+
+- **Discovery**: Marketplace listing for MCP servers
+- **Hosting**: Containerized deployment with auto-scaling
+- **Authentication UI**: OAuth flow presentation for users
+- **Session Configuration**: Per-user settings passed via URL parameters
+- **Observability**: Usage logs and monitoring
+
+### Current Architecture Limitations
+
+The current nextcloud-mcp-server architecture assumes a **self-hosted deployment** with:
+
+1. **Persistent Infrastructure**
+   - Qdrant vector database for semantic search
+   - Background sync worker for content indexing
+   - Refresh token storage for offline access
+
+2. **Single-Tenant Configuration**
+   - Environment variables configure one Nextcloud instance
+   - `NEXTCLOUD_HOST`, `NEXTCLOUD_USERNAME`, `NEXTCLOUD_PASSWORD`
+   - Or OAuth with a single IdP
+
+3. **Stateful Operations**
+   - Vector sync maintains index state across requests
+   - Token storage persists between sessions
+
+### Smithery Hosting Constraints
+
+Smithery-hosted containers are **stateless by design**:
+
+- No persistent storage between requests
+- No background workers or cron jobs
+- No databases (Qdrant, Redis, etc.)
+- Containers may be recycled at any time
+- Configuration passed per-session via URL parameters
+
+### Opportunity
+
+Many users have **publicly accessible Nextcloud instances** and want to:
+
+1. Try the MCP server without self-hosting infrastructure
+2. Connect multiple users to different Nextcloud instances
+3. Use basic Nextcloud tools without semantic search
+4. Benefit from Smithery's discovery and OAuth UI
+
+## Decision
+
+Implement a **stateless deployment mode** for Smithery that:
+
+1. **Disables stateful features** (vector sync, semantic search)
+2. **Creates clients per-session** from Smithery configuration
+3. **Supports multiple Nextcloud instances** via session config
+4. **Provides a useful subset of tools** that work without infrastructure
+
+### Architecture
+
+```
+┌─────────────────────────────────────────────────────────────────────────┐
+│                    Smithery-Hosted Stateless Mode                        │
+├─────────────────────────────────────────────────────────────────────────┤
+│                                                                          │
+│  MCP Client                    Smithery                                  │
+│  (Cursor, Claude)              Infrastructure                            │
+│        │                            │                                    │
+│        │ 1. Connect                 │                                    │
+│        ├───────────────────────────►│                                    │
+│        │                            │                                    │
+│        │ 2. Config UI               │                                    │
+│        │◄───────────────────────────┤  User enters:                      │
+│        │    (Smithery presents)     │  - nextcloud_url                   │
+│        │                            │  - auth_mode (basic/oauth)         │
+│        │                            │  - credentials                     │
+│        │ 3. Tool call               │                                    │
+│        ├───────────────────────────►│                                    │
+│        │    + session config        │                                    │
+│        │                            │                                    │
+│        │                    ┌───────┴───────┐                            │
+│        │                    │  MCP Server   │                            │
+│        │                    │  Container    │                            │
+│        │                    │               │                            │
+│        │                    │ 4. Create     │                            │
+│        │                    │    client     │                            │
+│        │                    │    from       │                            │
+│        │                    │    config     │                            │
+│        │                    │      │        │                            │
+│        │                    │      ▼        │                            │
+│        │                    │ 5. Call       │                            │
+│        │                    │    Nextcloud  │───────► User's Nextcloud   │
+│        │                    │    API        │         Instance           │
+│        │                    │      │        │                            │
+│        │                    │      ▼        │                            │
+│        │ 6. Response        │ Return result │                            │
+│        │◄───────────────────┤               │                            │
+│        │                    └───────────────┘                            │
+│                                                                          │
+└─────────────────────────────────────────────────────────────────────────┘
+```
+
+### Session Configuration Schema
+
+```python
+from pydantic import BaseModel, Field
+
+class SmitheryConfigSchema(BaseModel):
+    """Configuration schema for Smithery session."""
+
+    # Required: Nextcloud instance
+    nextcloud_url: str = Field(
+        ...,
+        description="Your Nextcloud instance URL (e.g., https://cloud.example.com)"
+    )
+
+    # Authentication mode
+    auth_mode: str = Field(
+        "app_password",
+        description="Authentication method: 'app_password' or 'oauth'"
+    )
+
+    # App Password authentication (recommended for Smithery)
+    username: str | None = Field(
+        None,
+        description="Nextcloud username (required for app_password auth)"
+    )
+    app_password: str | None = Field(
+        None,
+        description="Nextcloud app password (Settings → Security → App passwords)"
+    )
+
+    # OAuth authentication (advanced)
+    # When auth_mode='oauth', Smithery handles the OAuth flow
+    # and passes the access token automatically
+```
+
+### Feature Matrix
+
+| Feature | Self-Hosted | Smithery Stateless |
+|---------|-------------|-------------------|
+| **Notes** | | |
+| List/Search notes | ✓ | ✓ |
+| Get/Create/Update notes | ✓ | ✓ |
+| Semantic search | ✓ | ✗ |
+| **Calendar** | | |
+| List calendars | ✓ | ✓ |
+| Get/Create events | ✓ | ✓ |
+| **Contacts** | | |
+| List address books | ✓ | ✓ |
+| Search/Get contacts | ✓ | ✓ |
+| **Files (WebDAV)** | | |
+| List/Download files | ✓ | ✓ |
+| Upload files | ✓ | ✓ |
+| Search files | ✓ | ✓ (keyword only) |
+| **Deck** | | |
+| List boards/cards | ✓ | ✓ |
+| Create/Update cards | ✓ | ✓ |
+| **Tables** | | |
+| List/Query tables | ✓ | ✓ |
+| Create/Update rows | ✓ | ✓ |
+| **Cookbook** | | |
+| List/Get recipes | ✓ | ✓ |
+| **Semantic Search** | | |
+| Vector search | ✓ | ✗ |
+| RAG answers | ✓ | ✗ |
+| **Background Sync** | | |
+| Auto-indexing | ✓ | ✗ |
+| Webhook sync | ✓ | ✗ |
+| **Admin UI (`/app`)** | | |
+| Vector sync status | ✓ | ✗ |
+| Vector visualization | ✓ | ✗ |
+| Webhook management | ✓ | ✗ |
+| Session management | ✓ | ✗ |
+
+### Implementation
+
+#### 1. Deployment Mode Detection
+
+```python
+# nextcloud_mcp_server/config.py
+
+class DeploymentMode(Enum):
+    SELF_HOSTED = "self_hosted"      # Full features, env-based config
+    SMITHERY_STATELESS = "smithery"  # Stateless, session-based config
+
+def get_deployment_mode() -> DeploymentMode:
+    """Detect deployment mode from environment."""
+    if os.getenv("SMITHERY_DEPLOYMENT") == "true":
+        return DeploymentMode.SMITHERY_STATELESS
+    return DeploymentMode.SELF_HOSTED
+```
+
+#### 2. Session-Based Client Factory
+
+```python
+# nextcloud_mcp_server/context.py
+
+async def get_client(ctx: Context) -> NextcloudClient:
+    """Get NextcloudClient - from session config or environment."""
+
+    mode = get_deployment_mode()
+
+    if mode == DeploymentMode.SMITHERY_STATELESS:
+        # Create client from Smithery session config
+        config = ctx.session_config
+        if not config:
+            raise McpError("Session configuration required")
+
+        return NextcloudClient(
+            base_url=config.nextcloud_url,
+            username=config.username,
+            password=config.app_password,
+        )
+    else:
+        # Existing behavior: from environment or OAuth context
+        return await _get_client_from_context(ctx)
+```
+
+#### 3. Conditional Tool Registration
+
+```python
+# nextcloud_mcp_server/app.py
+
+def create_mcp_server(mode: DeploymentMode) -> FastMCP:
+    """Create MCP server with mode-appropriate tools."""
+
+    mcp = FastMCP("Nextcloud MCP")
+
+    # Always register core tools
+    configure_notes_tools(mcp)
+    configure_calendar_tools(mcp)
+    configure_contacts_tools(mcp)
+    configure_webdav_tools(mcp)
+    configure_deck_tools(mcp)
+    configure_tables_tools(mcp)
+    configure_cookbook_tools(mcp)
+
+    # Only register stateful tools in self-hosted mode
+    if mode == DeploymentMode.SELF_HOSTED:
+        configure_semantic_tools(mcp)  # Requires Qdrant
+        register_oauth_tools(mcp)       # Requires token storage
+
+    return mcp
+```
+
+#### 4. Exclude Admin UI Routes
+
+The `/app` admin UI should **not be installed** in Smithery mode because:
+
+- **Vector sync status** - No vector sync in stateless mode
+- **Vector visualization** - No Qdrant to visualize
+- **Webhook management** - No webhook sync without background workers
+- **Session management** - No persistent sessions to manage
+
+```python
+# nextcloud_mcp_server/app.py
+
+def create_app(mode: DeploymentMode) -> Starlette:
+    """Create Starlette app with mode-appropriate routes."""
+
+    routes = [
+        Route("/health/live", health_live, methods=["GET"]),
+        Route("/health/ready", health_ready, methods=["GET"]),
+    ]
+
+    # Only mount admin UI in self-hosted mode
+    if mode == DeploymentMode.SELF_HOSTED:
+        browser_app = create_browser_app()
+        routes.append(
+            Route("/app", lambda r: RedirectResponse("/app/", status_code=307))
+        )
+        routes.append(Mount("/app", app=browser_app))
+        logger.info("Admin UI mounted at /app")
+    else:
+        logger.info("Admin UI disabled in Smithery stateless mode")
+
+    # Mount FastMCP at root
+    mcp_app = create_mcp_server(mode).streamable_http_app()
+    routes.append(Mount("/", app=mcp_app))
+
+    return Starlette(routes=routes, lifespan=starlette_lifespan)
+```
+
+**Endpoints by Mode:**
+
+| Endpoint | Self-Hosted | Smithery |
+|----------|-------------|----------|
+| `/mcp` | ✓ | ✓ |
+| `/health/live` | ✓ | ✓ |
+| `/health/ready` | ✓ | ✓ |
+| `/.well-known/mcp-config` | ✓ | ✓ |
+| `/app` | ✓ | ✗ |
+| `/app/vector-sync/status` | ✓ | ✗ |
+| `/app/vector-viz` | ✓ | ✗ |
+| `/app/webhooks` | ✓ | ✗ |
+
+#### 5. Smithery Integration Files
+
+**smithery.yaml:**
+```yaml
+runtime: "container"
+build:
+  dockerfile: "Dockerfile.smithery"
+  dockerBuildPath: "."
+startCommand:
+  type: "http"
+  configSchema:
+    type: "object"
+    required: ["nextcloud_url", "username", "app_password"]
+    properties:
+      nextcloud_url:
+        type: "string"
+        title: "Nextcloud URL"
+        description: "Your Nextcloud instance URL (e.g., https://cloud.example.com)"
+      username:
+        type: "string"
+        title: "Username"
+        description: "Your Nextcloud username"
+      app_password:
+        type: "string"
+        title: "App Password"
+        description: "Generate at Settings → Security → App passwords"
+  exampleConfig:
+    nextcloud_url: "https://cloud.example.com"
+    username: "alice"
+    app_password: "xxxxx-xxxxx-xxxxx-xxxxx-xxxxx"
+```
+
+**Dockerfile.smithery:**
+```dockerfile
+FROM python:3.11-slim
+
+WORKDIR /app
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
+
+# Copy project files
+COPY pyproject.toml uv.lock ./
+COPY nextcloud_mcp_server ./nextcloud_mcp_server
+
+# Install dependencies (without vector/semantic extras)
+RUN uv sync --frozen --no-dev
+
+# Set Smithery mode
+ENV SMITHERY_DEPLOYMENT=true
+ENV VECTOR_SYNC_ENABLED=false
+
+# Smithery sets PORT=8081
+EXPOSE 8081
+
+CMD ["uv", "run", "python", "-m", "nextcloud_mcp_server.smithery_main"]
+```
+
+**nextcloud_mcp_server/smithery_main.py:**
+```python
+"""Smithery-specific entrypoint for stateless deployment."""
+
+import os
+import uvicorn
+from starlette.middleware.cors import CORSMiddleware
+
+from nextcloud_mcp_server.app import create_mcp_server
+from nextcloud_mcp_server.config import DeploymentMode
+
+def main():
+    # Force stateless mode
+    os.environ["SMITHERY_DEPLOYMENT"] = "true"
+    os.environ["VECTOR_SYNC_ENABLED"] = "false"
+
+    mcp = create_mcp_server(DeploymentMode.SMITHERY_STATELESS)
+    app = mcp.streamable_http_app()
+
+    # Add CORS for browser-based clients
+    app.add_middleware(
+        CORSMiddleware,
+        allow_origins=["*"],
+        allow_credentials=True,
+        allow_methods=["GET", "POST", "OPTIONS"],
+        allow_headers=["*"],
+        expose_headers=["mcp-session-id", "mcp-protocol-version"],
+    )
+
+    # Smithery sets PORT environment variable
+    port = int(os.environ.get("PORT", 8081))
+    uvicorn.run(app, host="0.0.0.0", port=port)
+
+if __name__ == "__main__":
+    main()
+```
+
+### Security Considerations
+
+1. **App Passwords over User Passwords**
+   - Smithery config encourages app passwords (revocable, scoped)
+   - Documentation guides users to create dedicated app passwords
+   - App passwords can be revoked without changing main password
+
+2. **HTTPS Required**
+   - `nextcloud_url` must be HTTPS for production use
+   - Validation rejects HTTP URLs in Smithery mode
+
+3. **No Credential Storage**
+   - Credentials exist only for request duration
+   - No server-side persistence of user credentials
+   - Smithery handles secure config transmission
+
+4. **Scope Limitation**
+   - Stateless mode cannot access offline_access
+   - No background operations on user's behalf
+   - Clear user expectation: tools work during session only
+
+### Migration Path
+
+Users can start with Smithery stateless mode and migrate to self-hosted:
+
+1. **Try on Smithery** → Basic tools, no setup
+2. **Self-host for semantic search** → Add Qdrant, enable vector sync
+3. **Full deployment** → Background sync, webhooks, multi-user OAuth
+
+## Consequences
+
+### Positive
+
+1. **Lower barrier to entry** - Users can try without infrastructure
+2. **Multi-user support** - Each session connects to different Nextcloud
+3. **Smithery ecosystem** - Discovery, observability, OAuth UI
+4. **Clear feature tiers** - Stateless (simple) vs self-hosted (full)
+
+### Negative
+
+1. **No semantic search** - Key differentiator unavailable on Smithery
+2. **Per-request auth** - Credentials sent with each request
+3. **No offline access** - Cannot perform background operations
+4. **Maintenance burden** - Two deployment modes to support
+
+### Neutral
+
+1. **Feature subset** - May encourage users to self-host for full features
+2. **Documentation needs** - Clear guidance on mode differences required
+
+## Alternatives Considered
+
+### 1. External MCP Only
+
+**Approach:** Only support self-hosted external MCP registration on Smithery.
+
+**Rejected because:**
+- Higher barrier to entry for new users
+- Misses opportunity for Smithery marketplace visibility
+- Users want to try before committing to infrastructure
+
+### 2. Embedded Vector DB (SQLite-vec)
+
+**Approach:** Use SQLite with vector extensions for per-request indexing.
+
+**Rejected because:**
+- No persistence between requests anyway
+- Indexing latency too high for synchronous requests
+- Complexity without benefit in stateless context
+
+### 3. External Vector DB Service
+
+**Approach:** Connect to Pinecone/Weaviate Cloud from Smithery container.
+
+**Rejected because:**
+- Adds external dependency and cost
+- Per-user collections require complex multi-tenancy
+- Sync still impossible without background workers
+
+### 4. Hybrid: Smithery + User's Qdrant
+
+**Approach:** User provides their own Qdrant URL in session config.
+
+**Considered for future:**
+- Could enable semantic search for advanced users
+- Adds complexity to session config
+- Sync still requires external trigger (manual or webhook)
+
+## References
+
+- [Smithery Documentation](https://smithery.ai/docs)
+- [Smithery Session Configuration](https://smithery.ai/docs/build/session-config)
+- [Smithery External MCPs](https://smithery.ai/docs/build/external)
+- [MCP Streamable HTTP Transport](https://modelcontextprotocol.io/docs/concepts/transports)
+- [Nextcloud App Passwords](https://docs.nextcloud.com/server/latest/user_manual/en/session_management.html#app-passwords)

nextcloud_mcp_server/app.py

@@ -3,6 +3,7 @@ import os
 import time
 from collections.abc import AsyncIterator
 from contextlib import AsyncExitStack, asynccontextmanager
+from contextvars import ContextVar
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, Optional
 
@@ -25,6 +26,8 @@ from starlette.middleware.cors import CORSMiddleware
 from starlette.responses import JSONResponse, RedirectResponse
 from starlette.routing import Mount, Route
 from starlette.staticfiles import StaticFiles
+from starlette.types import ASGIApp, Receive, Send
+from starlette.types import Scope as StarletteScope
 
 from nextcloud_mcp_server.auth import (
     InsufficientScopeError,
@@ -36,6 +39,8 @@ from nextcloud_mcp_server.auth import (
 from nextcloud_mcp_server.auth.unified_verifier import UnifiedTokenVerifier
 from nextcloud_mcp_server.client import NextcloudClient
 from nextcloud_mcp_server.config import (
+    DeploymentMode,
+    get_deployment_mode,
     get_document_processor_config,
     get_settings,
 )
@@ -122,6 +127,26 @@ def initialize_document_processors():
         except Exception as e:
             logger.warning(f"Failed to register Tesseract processor: {e}")
 
+    # Register PyMuPDF processor (high priority, local, no API required)
+    if "pymupdf" in config["processors"]:
+        pymupdf_config = config["processors"]["pymupdf"]
+        try:
+            from nextcloud_mcp_server.document_processors.pymupdf import (
+                PyMuPDFProcessor,
+            )
+
+            processor = PyMuPDFProcessor(
+                extract_images=pymupdf_config.get("extract_images", True),
+                image_dir=pymupdf_config.get("image_dir"),
+            )
+            registry.register(processor, priority=15)  # Higher than unstructured
+            logger.info(
+                f"Registered PyMuPDF processor: extract_images={pymupdf_config.get('extract_images', True)}"
+            )
+            registered_count += 1
+        except Exception as e:
+            logger.warning(f"Failed to register PyMuPDF processor: {e}")
+
     # Register custom processor
     if "custom" in config["processors"]:
         custom_config = config["processors"]["custom"]
@@ -244,17 +269,160 @@ class OAuthAppContext:
     )
 
 
+@dataclass
+class SmitheryAppContext:
+    """Application context for Smithery stateless mode.
+
+    ADR-016: No shared client - clients created per-request from session config.
+    """
+
+    pass  # No shared state needed - everything comes from session config
+
+
+# ADR-016: Smithery config schema for container runtime
+# This schema is served at /.well-known/mcp-config for Smithery discovery
+# See: https://smithery.ai/docs/build/session-config
+SMITHERY_CONFIG_SCHEMA = {
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "$id": "https://server.smithery.ai/nextcloud-mcp-server/.well-known/mcp-config",
+    "title": "Nextcloud MCP Server Configuration",
+    "description": "Configuration for connecting to your Nextcloud instance via app password authentication",
+    "x-query-style": "flat",  # Our schema has no nested objects, so flat style works
+    "type": "object",
+    "required": ["nextcloud_url", "username", "app_password"],
+    "properties": {
+        "nextcloud_url": {
+            "type": "string",
+            "title": "Nextcloud URL",
+            "description": "Your Nextcloud instance URL (e.g., https://cloud.example.com). Must be publicly accessible.",
+            "pattern": "^https?://.+",
+        },
+        "username": {
+            "type": "string",
+            "title": "Username",
+            "description": "Your Nextcloud username",
+            "minLength": 1,
+        },
+        "app_password": {
+            "type": "string",
+            "title": "App Password",
+            "description": "Nextcloud app password. Generate at Settings > Security > App passwords. Do NOT use your main password.",
+            "minLength": 1,
+        },
+    },
+    "additionalProperties": False,
+}
+
+
+# ADR-016: Context variable to hold Smithery session config per-request
+# This is set by SmitheryConfigMiddleware and accessed in context.py
+_smithery_session_config: ContextVar[dict[str, str] | None] = ContextVar(
+    "smithery_session_config"
+)
+_smithery_session_config.set(None)  # Set initial value
+
+
+def get_smithery_session_config() -> dict | None:
+    """Get the current Smithery session config from context variable.
+
+    Used by context.py to access config extracted from URL query parameters.
+    """
+    return _smithery_session_config.get()
+
+
+class SmitheryConfigMiddleware:
+    """Middleware to extract Smithery config from URL query parameters.
+
+    ADR-016: For container runtime, Smithery passes configuration as URL query
+    parameters to the /mcp endpoint. This middleware extracts those parameters
+    and stores them in a context variable for access in tools.
+
+    Configuration parameters:
+    - nextcloud_url: Nextcloud instance URL
+    - username: Nextcloud username
+    - app_password: Nextcloud app password
+
+    The extracted config is stored in a ContextVar and can be accessed via
+    get_smithery_session_config() in context.py.
+    """
+
+    def __init__(self, app: ASGIApp):
+        self.app = app
+
+    async def __call__(
+        self, scope: StarletteScope, receive: Receive, send: Send
+    ) -> None:
+        if scope["type"] == "http":
+            # Extract config from query parameters
+            from urllib.parse import parse_qs
+
+            query_string = scope.get("query_string", b"").decode("utf-8")
+            params = parse_qs(query_string)
+
+            # Build session config from query parameters
+            # Smithery uses dot notation for nested objects, but our schema is flat
+            session_config = {}
+            for key in ["nextcloud_url", "username", "app_password"]:
+                if key in params:
+                    # parse_qs returns lists, take first value
+                    session_config[key] = params[key][0]
+
+            # Store in context variable for access by context.py
+            if session_config:
+                _smithery_session_config.set(session_config)
+                logger.debug(
+                    f"Smithery config extracted: nextcloud_url={session_config.get('nextcloud_url')}, "
+                    f"username={session_config.get('username')}"
+                )
+
+        try:
+            await self.app(scope, receive, send)
+        finally:
+            # Clear context variable after request
+            _smithery_session_config.set(None)
+
+
+@asynccontextmanager
+async def app_lifespan_smithery(server: FastMCP) -> AsyncIterator[SmitheryAppContext]:
+    """
+    Manage application lifecycle for Smithery stateless mode.
+
+    ADR-016: Minimal lifespan with no shared state.
+    - No shared Nextcloud client (created per-request from session config)
+    - No vector sync (disabled in Smithery mode)
+    - No persistent storage (stateless deployment)
+    - No document processors (not enabled in Smithery mode)
+    """
+    logger.info("Starting MCP server in Smithery stateless mode")
+    logger.info("Clients will be created per-request from session config")
+
+    try:
+        yield SmitheryAppContext()
+    finally:
+        logger.info("Shutting down Smithery stateless mode")
+
+
 def is_oauth_mode() -> bool:
     """
     Determine if OAuth mode should be used.
 
     OAuth mode is enabled when:
     - NEXTCLOUD_USERNAME and NEXTCLOUD_PASSWORD are NOT set
+    - AND we are NOT in Smithery stateless mode
     - Or explicitly enabled via configuration
 
     Returns:
         True if OAuth mode, False if BasicAuth mode
     """
+    # ADR-016: Smithery stateless mode uses per-request BasicAuth from session config
+    # It's not OAuth mode even though env credentials aren't set
+    deployment_mode = get_deployment_mode()
+    if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+        logger.info(
+            "BasicAuth mode (Smithery stateless - credentials from session config)"
+        )
+        return False
+
     username = os.getenv("NEXTCLOUD_USERNAME")
     password = os.getenv("NEXTCLOUD_PASSWORD")
 
@@ -838,8 +1006,9 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
             "OpenTelemetry tracing disabled (set OTEL_EXPORTER_OTLP_ENDPOINT to enable)"
         )
 
-    # Determine authentication mode
+    # Determine authentication mode and deployment mode
     oauth_enabled = is_oauth_mode()
+    deployment_mode = get_deployment_mode()
 
     if oauth_enabled:
         logger.info("Configuring MCP server for OAuth mode")
@@ -900,8 +1069,17 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
             auth=auth_settings,
         )
     else:
-        logger.info("Configuring MCP server for BasicAuth mode")
-        mcp = FastMCP("Nextcloud MCP", lifespan=app_lifespan_basic)
+        # ADR-016: Use Smithery lifespan for stateless mode, BasicAuth otherwise
+        if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+            logger.info("Configuring MCP server for Smithery stateless mode")
+            # json_response=True returns plain JSON-RPC instead of SSE format,
+            # required for Smithery scanner compatibility
+            mcp = FastMCP(
+                "Nextcloud MCP", lifespan=app_lifespan_smithery, json_response=True
+            )
+        else:
+            logger.info("Configuring MCP server for BasicAuth mode")
+            mcp = FastMCP("Nextcloud MCP", lifespan=app_lifespan_basic)
 
     @mcp.resource("nc://capabilities")
     async def nc_get_capabilities():
@@ -937,8 +1115,12 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
             )
 
     # Register semantic search tools (cross-app feature)
+    # ADR-016: Skip in Smithery stateless mode (no vector database)
     settings = get_settings()
-    if settings.vector_sync_enabled:
+    deployment_mode = get_deployment_mode()
+    if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+        logger.info("Skipping semantic search tools (Smithery stateless mode)")
+    elif settings.vector_sync_enabled:
         logger.info("Configuring semantic search tools (vector sync enabled)")
         configure_semantic_tools(mcp)
     else:
@@ -1341,6 +1523,26 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
     )
     logger.info("Test webhook endpoint enabled: /webhooks/nextcloud")
 
+    # ADR-016: Add Smithery well-known config endpoint for container runtime discovery
+    if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+
+        def smithery_mcp_config(request):
+            """Smithery MCP configuration endpoint.
+
+            Returns JSON Schema for Smithery's configuration UI.
+            This endpoint is required for Smithery container runtime discovery.
+            """
+            return JSONResponse(SMITHERY_CONFIG_SCHEMA)
+
+        routes.append(
+            Route(
+                "/.well-known/mcp-config",
+                smithery_mcp_config,
+                methods=["GET"],
+            )
+        )
+        logger.info("Smithery config endpoint enabled: /.well-known/mcp-config")
+
     # Note: Metrics endpoint is NOT exposed on main HTTP port for security reasons.
     # Metrics are served on dedicated port via setup_metrics() (default: 9090)
 
@@ -1471,85 +1673,98 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
         )
 
     # Add user info routes (available in both BasicAuth and OAuth modes)
-    # These require session authentication, so we wrap them in a separate app
-    from nextcloud_mcp_server.auth.session_backend import SessionAuthBackend
-    from nextcloud_mcp_server.auth.userinfo_routes import (
-        revoke_session,
-        user_info_html,
-        vector_sync_status_fragment,
-    )
-    from nextcloud_mcp_server.auth.viz_routes import (
-        chunk_context_endpoint,
-        vector_visualization_html,
-        vector_visualization_search,
-    )
-    from nextcloud_mcp_server.auth.webhook_routes import (
-        disable_webhook_preset,
-        enable_webhook_preset,
-        webhook_management_pane,
-    )
-
-    # Create a separate Starlette app for browser routes that need session auth
-    # This prevents SessionAuthBackend from interfering with FastMCP's OAuth
-    browser_routes = [
-        Route("/", user_info_html, methods=["GET"]),  # /app → user info with all tabs
-        Route(
-            "/revoke", revoke_session, methods=["POST"], name="revoke_session_endpoint"
-        ),  # /app/revoke → revoke_session
-        # Vector sync status fragment (htmx polling)
-        Route(
-            "/vector-sync/status",
+    # ADR-016: Skip /app admin UI in Smithery stateless mode (no vector sync, webhooks)
+    if deployment_mode != DeploymentMode.SMITHERY_STATELESS:
+        # These require session authentication, so we wrap them in a separate app
+        from nextcloud_mcp_server.auth.session_backend import SessionAuthBackend
+        from nextcloud_mcp_server.auth.userinfo_routes import (
+            revoke_session,
+            user_info_html,
             vector_sync_status_fragment,
-            methods=["GET"],
-        ),  # /app/vector-sync/status
-        # Vector visualization routes
-        Route(
-            "/vector-viz", vector_visualization_html, methods=["GET"]
-        ),  # /app/vector-viz
-        Route(
-            "/vector-viz/search",
-            vector_visualization_search,
-            methods=["GET"],
-        ),  # /app/vector-viz/search
-        Route(
-            "/chunk-context",
-            chunk_context_endpoint,
-            methods=["GET"],
-        ),  # /app/chunk-context
-        # Webhook management routes (admin-only)
-        Route("/webhooks", webhook_management_pane, methods=["GET"]),  # /app/webhooks
-        Route(
-            "/webhooks/enable/{preset_id:str}", enable_webhook_preset, methods=["POST"]
-        ),
-        Route(
-            "/webhooks/disable/{preset_id:str}",
-            disable_webhook_preset,
-            methods=["DELETE"],
-        ),
-    ]
-
-    # Add static files mount if directory exists
-    static_dir = os.path.join(os.path.dirname(__file__), "auth", "static")
-    if os.path.isdir(static_dir):
-        browser_routes.append(
-            Mount("/static", StaticFiles(directory=static_dir), name="static")
         )
-        logger.info(f"Mounted static files from {static_dir}")
+        from nextcloud_mcp_server.auth.viz_routes import (
+            chunk_context_endpoint,
+            vector_visualization_html,
+            vector_visualization_search,
+        )
+        from nextcloud_mcp_server.auth.webhook_routes import (
+            disable_webhook_preset,
+            enable_webhook_preset,
+            webhook_management_pane,
+        )
 
-    browser_app = Starlette(routes=browser_routes)
-    browser_app.add_middleware(
-        AuthenticationMiddleware,  # type: ignore[invalid-argument-type]
-        backend=SessionAuthBackend(oauth_enabled=oauth_enabled),
-    )
+        # Create a separate Starlette app for browser routes that need session auth
+        # This prevents SessionAuthBackend from interfering with FastMCP's OAuth
+        browser_routes = [
+            Route(
+                "/", user_info_html, methods=["GET"]
+            ),  # /app → user info with all tabs
+            Route(
+                "/revoke",
+                revoke_session,
+                methods=["POST"],
+                name="revoke_session_endpoint",
+            ),  # /app/revoke → revoke_session
+            # Vector sync status fragment (htmx polling)
+            Route(
+                "/vector-sync/status",
+                vector_sync_status_fragment,
+                methods=["GET"],
+            ),  # /app/vector-sync/status
+            # Vector visualization routes
+            Route(
+                "/vector-viz", vector_visualization_html, methods=["GET"]
+            ),  # /app/vector-viz
+            Route(
+                "/vector-viz/search",
+                vector_visualization_search,
+                methods=["GET"],
+            ),  # /app/vector-viz/search
+            Route(
+                "/chunk-context",
+                chunk_context_endpoint,
+                methods=["GET"],
+            ),  # /app/chunk-context
+            # Webhook management routes (admin-only)
+            Route(
+                "/webhooks", webhook_management_pane, methods=["GET"]
+            ),  # /app/webhooks
+            Route(
+                "/webhooks/enable/{preset_id:str}",
+                enable_webhook_preset,
+                methods=["POST"],
+            ),
+            Route(
+                "/webhooks/disable/{preset_id:str}",
+                disable_webhook_preset,
+                methods=["DELETE"],
+            ),
+        ]
 
-    # Add redirect from /app to /app/ (Starlette requires trailing slash for mounted apps)
-    routes.append(
-        Route("/app", lambda request: RedirectResponse("/app/", status_code=307))
-    )
+        # Add static files mount if directory exists
+        static_dir = os.path.join(os.path.dirname(__file__), "auth", "static")
+        if os.path.isdir(static_dir):
+            browser_routes.append(
+                Mount("/static", StaticFiles(directory=static_dir), name="static")
+            )
+            logger.info(f"Mounted static files from {static_dir}")
 
-    # Mount browser app at /app (webapp and admin routes)
-    routes.append(Mount("/app", app=browser_app))
-    logger.info("App routes with session auth: /app, /app/webhooks, /app/revoke")
+        browser_app = Starlette(routes=browser_routes)
+        browser_app.add_middleware(
+            AuthenticationMiddleware,  # type: ignore[invalid-argument-type]
+            backend=SessionAuthBackend(oauth_enabled=oauth_enabled),
+        )
+
+        # Add redirect from /app to /app/ (Starlette requires trailing slash for mounted apps)
+        routes.append(
+            Route("/app", lambda request: RedirectResponse("/app/", status_code=307))
+        )
+
+        # Mount browser app at /app (webapp and admin routes)
+        routes.append(Mount("/app", app=browser_app))
+        logger.info("App routes with session auth: /app, /app/webhooks, /app/revoke")
+    else:
+        logger.info("Admin UI (/app) disabled in Smithery stateless mode")
 
     # Mount FastMCP at root last (catch-all, handles OAuth via token_verifier)
     routes.append(Mount("/", app=mcp_app))
@@ -1669,4 +1884,11 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
 
         logger.info("WWW-Authenticate scope challenge handler enabled")
 
+    # ADR-016: Apply SmitheryConfigMiddleware in Smithery stateless mode
+    # This must be the outermost middleware to extract config from URL query parameters
+    # before any other middleware processes the request
+    if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+        app = SmitheryConfigMiddleware(app)
+        logger.info("SmitheryConfigMiddleware enabled for query parameter config")
+
     return app

nextcloud_mcp_server/auth/static/vector-viz.css

@@ -190,3 +190,30 @@
     color: var(--color-text-maxcontrast);
     font-style: italic;
 }
+
+/* PDF highlighted image styles */
+.chunk-image-container {
+    margin-bottom: 16px;
+    border: 1px solid var(--color-border);
+    border-radius: var(--border-radius);
+    overflow: hidden;
+    background: #fff;
+}
+.chunk-image-header {
+    background: var(--color-background-dark);
+    padding: 8px 12px;
+    font-size: 12px;
+    font-weight: 500;
+    color: var(--color-text-maxcontrast);
+    border-bottom: 1px solid var(--color-border);
+    font-family: var(--font-face);
+}
+.chunk-highlighted-image {
+    display: block;
+    max-width: 100%;
+    height: auto;
+    cursor: zoom-in;
+}
+.chunk-highlighted-image:hover {
+    opacity: 0.95;
+}

nextcloud_mcp_server/auth/static/vector-viz.js

@@ -217,7 +217,7 @@ function vizApp() {
         },
 
         async toggleChunk(result) {
-            const resultKey = `${result.doc_type}_${result.id}`;
+            const resultKey = `${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`;
 
             if (this.isChunkExpanded(resultKey)) {
                 delete this.expandedChunks[resultKey];

nextcloud_mcp_server/auth/templates/vector_viz.html

@@ -117,12 +117,13 @@
 
         <template x-if="!loading && results.length > 0">
             <div x-transition.opacity.duration.200ms>
-                <template x-for="result in results" :key="result.id">
+                <template x-for="result in results" :key="`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`">
                     <div style="padding: 12px; border-bottom: 1px solid #eee;">
                         <a :href="getNextcloudUrl(result)" target="_blank" style="font-weight: 500; color: #0066cc; text-decoration: none;">
                             <span x-text="result.title"></span>
                         </a>
-                        <div style="font-size: 14px; color: #666; margin-top: 4px;" x-text="result.excerpt"></div>
+                        <div style="font-size: 14px; color: #666; margin-top: 4px;"
+                             x-text="result.excerpt.length > 200 ? result.excerpt.substring(0, 200) + '...' : result.excerpt"></div>
                         <div style="font-size: 12px; color: #999; margin-top: 4px;">
                             Raw Score: <span x-text="result.original_score.toFixed(3)"></span>
                             (<span x-text="(result.score * 100).toFixed(0)"></span>% relative) |
@@ -134,22 +135,36 @@
                             <button
                                 class="chunk-toggle-btn"
                                 @click="toggleChunk(result)"
-                                x-text="isChunkExpanded(`${result.doc_type}_${result.id}`) ? 'Hide Chunk' : 'Show Chunk'"
+                                x-text="isChunkExpanded(`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`) ? 'Hide Chunk' : 'Show Chunk'"
                             ></button>
                         </template>
 
                         <!-- Chunk context (expanded inline) -->
-                        <template x-if="isChunkExpanded(`${result.doc_type}_${result.id}`)">
+                        <template x-if="isChunkExpanded(`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`)">
                             <div class="chunk-context" x-transition.opacity.duration.200ms>
-                                <template x-if="chunkLoading[`${result.doc_type}_${result.id}`]">
+                                <template x-if="chunkLoading[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]">
                                     <div style="color: #666; font-style: italic;">Loading chunk...</div>
                                 </template>
-                                <template x-if="!chunkLoading[`${result.doc_type}_${result.id}`]">
+                                <template x-if="!chunkLoading[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]">
                                     <div>
-                                        <template x-if="expandedChunks[`${result.doc_type}_${result.id}`]?.has_more_before">
+                                        <!-- Highlighted page image for PDFs -->
+                                        <template x-if="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.highlighted_page_image">
+                                            <div class="chunk-image-container">
+                                                <div class="chunk-image-header">
+                                                    <span>Page <span x-text="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.page_number"></span></span>
+                                                </div>
+                                                <img
+                                                    :src="'data:image/png;base64,' + expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.highlighted_page_image"
+                                                    :alt="'Page ' + expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.page_number"
+                                                    class="chunk-highlighted-image"
+                                                />
+                                            </div>
+                                        </template>
+                                        <!-- Text context -->
+                                        <template x-if="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.has_more_before">
                                             <span class="chunk-ellipsis">...</span>
                                         </template>
-                                        <span class="chunk-text" x-text="expandedChunks[`${result.doc_type}_${result.id}`]?.before_context"></span><span class="chunk-matched" x-text="expandedChunks[`${result.doc_type}_${result.id}`]?.chunk_text"></span><span class="chunk-text" x-text="expandedChunks[`${result.doc_type}_${result.id}`]?.after_context"></span><template x-if="expandedChunks[`${result.doc_type}_${result.id}`]?.has_more_after">
+                                        <span class="chunk-text" x-text="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.before_context"></span><span class="chunk-matched" x-text="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.chunk_text"></span><span class="chunk-text" x-text="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.after_context"></span><template x-if="expandedChunks[`${result.doc_type}_${result.id}_${result.chunk_start_offset || 0}`]?.has_more_after">
                                             <span class="chunk-ellipsis">...</span>
                                         </template>
                                     </div>

nextcloud_mcp_server/auth/userinfo_routes.py

@@ -18,6 +18,8 @@ from starlette.authentication import requires
 from starlette.requests import Request
 from starlette.responses import HTMLResponse, JSONResponse
 
+from nextcloud_mcp_server.client import NextcloudClient
+
 logger = logging.getLogger(__name__)
 
 # Setup Jinja2 environment for templates
@@ -25,14 +27,20 @@ _template_dir = Path(__file__).parent / "templates"
 _jinja_env = Environment(loader=FileSystemLoader(_template_dir))
 
 
-async def _get_authenticated_client_for_userinfo(request: Request) -> httpx.AsyncClient:
-    """Get an authenticated HTTP client for user info page operations.
+async def _get_authenticated_client_for_userinfo(request: Request) -> NextcloudClient:
+    """Get an authenticated Nextcloud client for user info page operations.
+
+    This is a shared helper for authenticated routes that need to access
+    Nextcloud APIs. It handles both BasicAuth and OAuth authentication modes.
 
     Args:
         request: Starlette request object
 
     Returns:
-        Authenticated httpx.AsyncClient
+        Authenticated NextcloudClient
+
+    Raises:
+        RuntimeError: If credentials/session not configured
     """
     oauth_ctx = getattr(request.app.state, "oauth_context", None)
 
@@ -45,11 +53,15 @@ async def _get_authenticated_client_for_userinfo(request: Request) -> httpx.Asyn
         if not all([nextcloud_host, username, password]):
             raise RuntimeError("BasicAuth credentials not configured")
 
-        assert nextcloud_host is not None  # Type narrowing for type checker
-        return httpx.AsyncClient(
+        from httpx import BasicAuth
+
+        assert nextcloud_host is not None
+        assert username is not None
+        assert password is not None
+        return NextcloudClient(
             base_url=nextcloud_host,
-            auth=(username, password),
-            timeout=30.0,
+            username=username,
+            auth=BasicAuth(username, password),
         )
 
     # OAuth mode - get token from session
@@ -64,15 +76,14 @@ async def _get_authenticated_client_for_userinfo(request: Request) -> httpx.Asyn
         raise RuntimeError("No access token found in session")
 
     access_token = token_data["access_token"]
+    username = token_data.get("username")
     nextcloud_host = oauth_ctx.get("config", {}).get("nextcloud_host", "")
 
-    if not nextcloud_host:
-        raise RuntimeError("Nextcloud host not configured")
+    if not nextcloud_host or not username:
+        raise RuntimeError("Nextcloud host or username not configured")
 
-    return httpx.AsyncClient(
-        base_url=nextcloud_host,
-        headers={"Authorization": f"Bearer {access_token}"},
-        timeout=30.0,
+    return NextcloudClient.from_token(
+        base_url=nextcloud_host, token=access_token, username=username
     )
 
 
@@ -423,10 +434,10 @@ async def user_info_html(request: Request) -> HTMLResponse:
     try:
         from nextcloud_mcp_server.auth.permissions import is_nextcloud_admin
 
-        # Get authenticated HTTP client
-        http_client = await _get_authenticated_client_for_userinfo(request)
-        is_admin = await is_nextcloud_admin(request, http_client)
-        await http_client.aclose()
+        # Get authenticated Nextcloud client
+        nc_client = await _get_authenticated_client_for_userinfo(request)
+        is_admin = await is_nextcloud_admin(request, nc_client._client)
+        await nc_client.close()
     except Exception as e:
         logger.warning(f"Failed to check admin status: {e}")
         # Default to not admin if check fails

nextcloud_mcp_server/auth/viz_routes.py

@@ -27,6 +27,7 @@ from nextcloud_mcp_server.search import (
     SemanticSearchAlgorithm,
 )
 from nextcloud_mcp_server.vector.pca import PCA
+from nextcloud_mcp_server.vector.placeholder import get_placeholder_filter
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
 logger = logging.getLogger(__name__)
@@ -138,7 +139,7 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
             _get_authenticated_client_for_userinfo,
         )
 
-        async with await _get_authenticated_client_for_userinfo(request) as http_client:  # noqa: F841
+        async with await _get_authenticated_client_for_userinfo(request) as nc_client:  # noqa: F841
             # Create search algorithm (no client needed - verification removed)
             if algorithm == "semantic":
                 search_algo = SemanticSearchAlgorithm(score_threshold=score_threshold)
@@ -212,75 +213,51 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
                     "success": True,
                     "results": [],
                     "coordinates_3d": [],
-                    "query_coords": None,
+                    "query_coords": [],
                     "message": "No results found",
                 }
             )
 
-        # Fetch vectors for matching results from Qdrant
+        # Fetch vectors for specific matching chunks from Qdrant using batch retrieve
         vector_fetch_start = time.perf_counter()
         qdrant_client = await get_qdrant_client()
-        doc_ids = [r.id for r in search_results]
 
-        # Retrieve vectors for the matching documents
-        from qdrant_client.models import FieldCondition, Filter, MatchAny
+        chunk_vectors_map = {}  # Map (doc_id, chunk_start, chunk_end) -> vector
 
-        points_response = await qdrant_client.scroll(
-            collection_name=settings.get_collection_name(),
-            scroll_filter=Filter(
-                must=[
-                    FieldCondition(
-                        key="doc_id",
-                        match=MatchAny(any=[str(doc_id) for doc_id in doc_ids]),
-                    ),
-                    FieldCondition(
-                        key="user_id",
-                        match={"value": username},
-                    ),
-                ]
-            ),
-            limit=len(doc_ids) * 2,  # Account for multiple chunks per doc
-            with_vectors=["dense"],  # Only fetch dense vectors for visualization
-            with_payload=["doc_id"],  # Need doc_id to map vectors to results
-        )
+        # Collect point IDs from search results for batch retrieval
+        # point_id is the Qdrant internal ID returned by search algorithms
+        point_ids = [r.point_id for r in search_results if r.point_id]
 
-        points = points_response[0]
-
-        if not points:
-            return JSONResponse(
-                {
-                    "success": True,
-                    "results": [],
-                    "coordinates_2d": [],
-                    "message": "No vectors found for results",
-                }
+        if point_ids:
+            # Single batch retrieve call instead of N sequential scroll calls
+            # This is ~50x faster for 50 results (1 HTTP request vs 50)
+            points_response = await qdrant_client.retrieve(
+                collection_name=settings.get_collection_name(),
+                ids=point_ids,
+                with_vectors=["dense"],
+                with_payload=["doc_id", "chunk_start_offset", "chunk_end_offset"],
             )
 
-        # Extract dense vectors and group by document
-        def extract_dense_vector(point):
-            if point.vector is None:
-                return None
-            # If named vectors (dict), extract "dense"
-            if isinstance(point.vector, dict):
-                return point.vector.get("dense")
-            # If unnamed vector (array), use directly
-            return point.vector
+            # Build chunk_vectors_map from batch response
+            for point in points_response:
+                if point.vector is not None:
+                    # Extract dense vector (handle both named and unnamed vectors)
+                    if isinstance(point.vector, dict):
+                        vector = point.vector.get("dense")
+                    else:
+                        vector = point.vector
 
-        # Group chunk vectors by doc_id
-        from collections import defaultdict
-
-        doc_chunks = defaultdict(list)
-        for point in points:
-            if point.payload:
-                doc_id = int(point.payload.get("doc_id", 0))
-                vector = extract_dense_vector(point)
-                if vector is not None:
-                    doc_chunks[doc_id].append(vector)
+                    if vector is not None and point.payload:
+                        doc_id = point.payload.get("doc_id")
+                        chunk_start = point.payload.get("chunk_start_offset")
+                        chunk_end = point.payload.get("chunk_end_offset")
+                        chunk_key = (doc_id, chunk_start, chunk_end)
+                        chunk_vectors_map[chunk_key] = vector
 
         vector_fetch_duration = time.perf_counter() - vector_fetch_start
 
-        if len(doc_chunks) < 2:
-            # Not enough documents for PCA
+        if len(chunk_vectors_map) < 2:
+            # Not enough chunks for PCA
             return JSONResponse(
                 {
                     "success": True,
@@ -296,15 +273,15 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
                     ],
                     "coordinates_3d": [[0, 0, 0]] * len(search_results),
                     "query_coords": [0, 0, 0],
-                    "message": "Not enough documents for PCA",
+                    "message": "Not enough chunks for PCA",
                 }
             )
 
         # Detect embedding dimension from first available vector
         embedding_dim = None
-        for chunks in doc_chunks.values():
-            if chunks:
-                embedding_dim = len(chunks[0])
+        for vector in chunk_vectors_map.values():
+            if vector is not None:
+                embedding_dim = len(vector)
                 break
 
         if embedding_dim is None:
@@ -318,37 +295,42 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
 
         logger.info(f"Detected embedding dimension: {embedding_dim}")
 
-        # Average chunk vectors per document to create document-level embeddings
-        # Maintain order of search_results for coordinate mapping
-        doc_vectors = []
+        # Build chunk vectors array in search_results order (1:1 mapping)
+        chunk_vectors = []
         for result in search_results:
-            if result.id in doc_chunks:
-                # Average all chunk embeddings for this document
-                chunk_vectors = np.array(doc_chunks[result.id])
-                avg_vector = np.mean(chunk_vectors, axis=0)
-                doc_vectors.append(avg_vector)
-                logger.debug(f"Doc {result.id}: averaged {len(chunk_vectors)} chunks")
+            chunk_key = (result.id, result.chunk_start_offset, result.chunk_end_offset)
+            if chunk_key in chunk_vectors_map:
+                chunk_vectors.append(chunk_vectors_map[chunk_key])
             else:
-                # Document not found in vectors (shouldn't happen)
-                logger.warning(f"Doc {result.id} not found in fetched vectors")
-                # Use zero vector as fallback with detected dimension
-                doc_vectors.append(np.zeros(embedding_dim))
+                # Chunk not found in vectors (shouldn't happen)
+                logger.warning(
+                    f"Chunk {chunk_key} not found in fetched vectors, using zero vector"
+                )
+                # Use zero vector as fallback
+                chunk_vectors.append(np.zeros(embedding_dim))
 
-        doc_vectors = np.array(doc_vectors)
+        chunk_vectors = np.array(chunk_vectors)
 
-        # Generate query embedding for visualization
+        # Reuse query embedding from search algorithm (avoids redundant embedding call)
         query_embed_start = time.perf_counter()
-        from nextcloud_mcp_server.embedding.service import get_embedding_service
+        if search_algo.query_embedding is not None:
+            query_embedding = search_algo.query_embedding
+            logger.info(
+                f"Reusing query embedding from search algorithm "
+                f"(dimension={len(query_embedding)})"
+            )
+        else:
+            # Fallback: generate embedding if not available from search
+            from nextcloud_mcp_server.embedding.service import get_embedding_service
 
-        embedding_service = get_embedding_service()
-        query_embedding = await embedding_service.embed(query)
+            embedding_service = get_embedding_service()
+            query_embedding = await embedding_service.embed(query)
+            logger.info(f"Generated query embedding (dimension={len(query_embedding)})")
         query_embed_duration = time.perf_counter() - query_embed_start
 
-        logger.info(f"Generated query embedding (dimension={len(query_embedding)})")
-
-        # Combine query vector with document vectors for PCA
+        # Combine query vector with chunk vectors for PCA
         # Query will be the last point in the array
-        all_vectors = np.vstack([doc_vectors, np.array([query_embedding])])
+        all_vectors = np.vstack([chunk_vectors, np.array([query_embedding])])
 
         # Normalize vectors to unit length (L2 normalization)
         # This is critical because Qdrant uses COSINE distance, which only measures
@@ -375,9 +357,19 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
         )
 
         # Apply PCA dimensionality reduction (768-dim → 3D) on normalized vectors
+        # Run in thread pool to avoid blocking the event loop (CPU-bound)
         pca_start = time.perf_counter()
-        pca = PCA(n_components=3)
-        coords_3d = pca.fit_transform(all_vectors_normalized)
+
+        def _compute_pca(vectors: np.ndarray) -> tuple[np.ndarray, PCA]:
+            pca = PCA(n_components=3)
+            coords = pca.fit_transform(vectors)
+            return coords, pca
+
+        import anyio
+
+        coords_3d, pca = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+            lambda: _compute_pca(all_vectors_normalized)
+        )
         pca_duration = time.perf_counter() - pca_start
 
         # After fit, these attributes are guaranteed to be set
@@ -394,17 +386,12 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
             # Replace NaN with 0 to allow JSON serialization
             coords_3d = np.nan_to_num(coords_3d, nan=0.0)
 
-        # Split query coords from document coords
+        # Split query coords from chunk coords
         # Round to 2 decimal places for cleaner display
         query_coords_3d = [
             round(float(x), 2) for x in coords_3d[-1]
         ]  # Last point is query
-        doc_coords_3d = coords_3d[:-1]  # All but last are documents
-
-        total_chunks = sum(len(chunks) for chunks in doc_chunks.values())
-        avg_chunks_per_doc = (
-            total_chunks / len(doc_vectors) if doc_vectors.size > 0 else 0
-        )
+        chunk_coords_3d = coords_3d[:-1]  # All but last are chunks
 
         logger.info(
             f"PCA explained variance: PC1={pca.explained_variance_ratio_[0]:.3f}, "
@@ -412,13 +399,14 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
             f"PC3={pca.explained_variance_ratio_[2]:.3f}"
         )
         logger.info(
-            f"Embedding stats: documents={len(doc_vectors)}, "
-            f"total_chunks={total_chunks}, avg_chunks_per_doc={avg_chunks_per_doc:.1f}, "
-            f"query_dim={len(query_embedding)}, doc_vector_dim={doc_vectors.shape[1] if doc_vectors.size > 0 else 0}"
+            f"Embedding stats: chunks={len(chunk_vectors)}, "
+            f"query_dim={len(query_embedding)}, chunk_vector_dim={chunk_vectors.shape[1] if chunk_vectors.size > 0 else 0}"
         )
 
         # Coordinates already match search_results order (1:1 mapping)
-        result_coords = [[round(float(x), 2) for x in coord] for coord in doc_coords_3d]
+        result_coords = [
+            [round(float(x), 2) for x in coord] for coord in chunk_coords_3d
+        ]
 
         # Build response
         response_results = [
@@ -447,7 +435,7 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
             f"vector_fetch={vector_fetch_duration * 1000:.1f}ms ({vector_fetch_duration / total_duration * 100:.1f}%), "
             f"query_embed={query_embed_duration * 1000:.1f}ms ({query_embed_duration / total_duration * 100:.1f}%), "
             f"pca={pca_duration * 1000:.1f}ms ({pca_duration / total_duration * 100:.1f}%), "
-            f"results={len(search_results)}, doc_vectors={len(doc_vectors)}"
+            f"results={len(search_results)}, chunk_vectors={len(chunk_vectors)}"
         )
 
         return JSONResponse(
@@ -468,7 +456,7 @@ async def vector_visualization_search(request: Request) -> JSONResponse:
                     "query_embed_ms": round(query_embed_duration * 1000, 2),
                     "pca_ms": round(pca_duration * 1000, 2),
                     "num_results": len(search_results),
-                    "num_doc_vectors": len(doc_vectors),
+                    "num_chunk_vectors": len(chunk_vectors),
                 },
             }
         )
@@ -517,77 +505,118 @@ async def chunk_context_endpoint(request: Request) -> JSONResponse:
                 status_code=400,
             )
 
+        # Type assertions - we validated these above
+        assert doc_type is not None
+        assert doc_id is not None
+        assert start_str is not None
+        assert end_str is not None
+
         start = int(start_str)
         end = int(end_str)
+        # Convert doc_id to int (all document types use int IDs)
+        doc_id_int = int(doc_id)
 
-        # Currently only support notes
-        if doc_type != "note":
-            return JSONResponse(
-                {"success": False, "error": f"Unsupported doc_type: {doc_type}"},
-                status_code=400,
-            )
-
-        # Get authenticated HTTP client and fetch note
+        # Get authenticated Nextcloud client
         from nextcloud_mcp_server.auth.userinfo_routes import (
             _get_authenticated_client_for_userinfo,
         )
-        from nextcloud_mcp_server.client.notes import NotesClient
+        from nextcloud_mcp_server.search.context import get_chunk_with_context
 
-        # Get username from request auth
-        username = (
-            request.user.display_name
-            if hasattr(request.user, "display_name")
-            else "unknown"
-        )
+        # Use context expansion module to fetch chunk with surrounding context
+        async with await _get_authenticated_client_for_userinfo(request) as nc_client:
+            chunk_context = await get_chunk_with_context(
+                nc_client=nc_client,
+                user_id=request.user.display_name,  # User ID from auth
+                doc_id=doc_id_int,
+                doc_type=doc_type,
+                chunk_start=start,
+                chunk_end=end,
+                context_chars=context_chars,
+            )
 
-        # Create notes client with authenticated HTTP client
-        http_client = await _get_authenticated_client_for_userinfo(request)
-        notes_client = NotesClient(http_client, username)
-
-        # Fetch full note content
-        note = await notes_client.get_note(int(doc_id))
-        full_content = f"{note['title']}\n\n{note['content']}"
-
-        # Validate offsets
-        if start < 0 or end > len(full_content) or start >= end:
+        # Check if context expansion succeeded
+        if chunk_context is None:
             return JSONResponse(
                 {
                     "success": False,
-                    "error": f"Invalid offsets: start={start}, end={end}, content_length={len(full_content)}",
+                    "error": f"Failed to fetch chunk context for {doc_type} {doc_id}",
                 },
-                status_code=400,
+                status_code=404,
             )
 
-        # Extract chunk
-        chunk_text = full_content[start:end]
-
-        # Extract context before and after
-        before_start = max(0, start - context_chars)
-        before_context = full_content[before_start:start]
-
-        after_end = min(len(full_content), end + context_chars)
-        after_context = full_content[end:after_end]
-
-        # Determine if there's more content
-        has_more_before = before_start > 0
-        has_more_after = after_end < len(full_content)
-
         logger.info(
             f"Fetched chunk context for {doc_type}_{doc_id}: "
-            f"chunk_len={len(chunk_text)}, before_len={len(before_context)}, "
-            f"after_len={len(after_context)}"
+            f"chunk_len={len(chunk_context.chunk_text)}, "
+            f"before_len={len(chunk_context.before_context)}, "
+            f"after_len={len(chunk_context.after_context)}"
         )
 
-        return JSONResponse(
-            {
-                "success": True,
-                "chunk_text": chunk_text,
-                "before_context": before_context,
-                "after_context": after_context,
-                "has_more_before": has_more_before,
-                "has_more_after": has_more_after,
-            }
-        )
+        # For PDF files, also fetch the highlighted page image from Qdrant
+        highlighted_page_image = None
+        page_number = None
+        if doc_type == "file":
+            try:
+                from qdrant_client.models import FieldCondition, Filter, MatchValue
+
+                settings = get_settings()
+                qdrant_client = await get_qdrant_client()
+                username = request.user.display_name
+
+                # Query for this specific chunk's highlighted image
+                points_response = await qdrant_client.scroll(
+                    collection_name=settings.get_collection_name(),
+                    scroll_filter=Filter(
+                        must=[
+                            get_placeholder_filter(),
+                            FieldCondition(
+                                key="doc_id", match=MatchValue(value=doc_id_int)
+                            ),
+                            FieldCondition(
+                                key="user_id", match=MatchValue(value=username)
+                            ),
+                            FieldCondition(
+                                key="chunk_start_offset", match=MatchValue(value=start)
+                            ),
+                            FieldCondition(
+                                key="chunk_end_offset", match=MatchValue(value=end)
+                            ),
+                        ]
+                    ),
+                    limit=1,
+                    with_vectors=False,
+                    with_payload=["highlighted_page_image", "page_number"],
+                )
+
+                points = points_response[0]
+                if points and points[0].payload:
+                    highlighted_page_image = points[0].payload.get(
+                        "highlighted_page_image"
+                    )
+                    page_number = points[0].payload.get("page_number")
+                    if highlighted_page_image:
+                        logger.info(
+                            f"Found highlighted image for chunk: "
+                            f"page={page_number}, image_size={len(highlighted_page_image)}"
+                        )
+            except Exception as e:
+                logger.warning(f"Failed to fetch highlighted image: {e}")
+
+        # Return response compatible with frontend expectations
+        response_data: dict = {
+            "success": True,
+            "chunk_text": chunk_context.chunk_text,
+            "before_context": chunk_context.before_context,
+            "after_context": chunk_context.after_context,
+            "has_more_before": chunk_context.has_before_truncation,
+            "has_more_after": chunk_context.has_after_truncation,
+        }
+
+        # Add image data if available
+        if highlighted_page_image:
+            response_data["highlighted_page_image"] = highlighted_page_image
+            response_data["page_number"] = page_number
+
+        return JSONResponse(response_data)
 
     except ValueError as e:
         logger.error(f"Invalid parameter format: {e}")

nextcloud_mcp_server/client/__init__.py

@@ -130,10 +130,75 @@ class NextcloudClient:
         all_notes = self.notes.get_all_notes()
         return await self._notes_search.search_notes(all_notes, query)
 
+    async def find_files_by_tag(
+        self, tag_name: str, mime_type_filter: str | None = None
+    ) -> list[dict]:
+        """Find files by system tag name, optionally filtered by MIME type.
+
+        This method coordinates tag lookup and file retrieval via WebDAV:
+        1. Look up the tag ID by name
+        2. Get all files with that tag (via REPORT with full metadata)
+        3. Optionally filter by MIME type
+
+        Args:
+            tag_name: Name of the system tag to search for (e.g., "vector-index")
+            mime_type_filter: Optional MIME type filter (e.g., "application/pdf")
+
+        Returns:
+            List of file dictionaries with WebDAV properties (path, size, content_type, etc.)
+
+        Raises:
+            RuntimeError: If tag lookup or file query fails
+
+        Examples:
+            # Find all files with "vector-index" tag
+            files = await nc_client.find_files_by_tag("vector-index")
+
+            # Find only PDFs with the tag
+            pdfs = await nc_client.find_files_by_tag("vector-index", "application/pdf")
+        """
+        # Look up tag by name using WebDAV
+        tag = await self.webdav.get_tag_by_name(tag_name)
+        if not tag:
+            logger.debug(f"Tag '{tag_name}' not found, returning empty list")
+            return []
+
+        # Get files with this tag (returns full file info from REPORT)
+        files = await self.webdav.get_files_by_tag(tag["id"])
+        if not files:
+            logger.debug(f"No files found with tag '{tag_name}'")
+            return []
+
+        logger.debug(f"Found {len(files)} files with tag '{tag_name}'")
+
+        # Apply MIME type filter if specified
+        if mime_type_filter:
+            filtered_files = [
+                f
+                for f in files
+                if f.get("content_type", "").startswith(mime_type_filter)
+            ]
+            logger.info(
+                f"Returning {len(filtered_files)} files with tag '{tag_name}' (filtered by {mime_type_filter})"
+            )
+            return filtered_files
+
+        logger.info(f"Returning {len(files)} files with tag '{tag_name}'")
+        return files
+
     def _get_webdav_base_path(self) -> str:
         """Helper to get the base WebDAV path for the authenticated user."""
         return f"/remote.php/dav/files/{self.username}"
 
+    async def __aenter__(self):
+        """Async context manager entry."""
+        return self
+
+    async def __aexit__(self, exc_type, exc_val, exc_tb):
+        """Async context manager exit - closes all clients."""
+        await self.close()
+        return False  # Don't suppress exceptions
+
     async def close(self):
         """Close the HTTP client and CalDAV client."""
         await self._client.aclose()

nextcloud_mcp_server/client/webdav.py

@@ -821,6 +821,20 @@ class WebDAVClient(BaseNextcloudClient):
                     item["file_id"] = int(value) if value else None
                 elif tag == "favorite":
                     item["is_favorite"] = value == "1"
+                elif tag == "tags":
+                    # Tags can be comma-separated or have multiple child elements
+                    if value:
+                        # Handle comma-separated tags
+                        item["tags"] = [
+                            t.strip() for t in value.split(",") if t.strip()
+                        ]
+                    else:
+                        # Check for child tag elements (alternative format)
+                        tag_elements = child.findall(".//{http://owncloud.org/ns}tag")
+                        if tag_elements:
+                            item["tags"] = [t.text for t in tag_elements if t.text]
+                        else:
+                            item["tags"] = []
                 elif tag == "permissions":
                     item["permissions"] = value
                 elif tag == "size":
@@ -948,3 +962,336 @@ class WebDAVClient(BaseNextcloudClient):
             properties=properties,
             limit=limit,
         )
+
+    async def find_by_tag(
+        self, tag_name: str, scope: str = "", limit: Optional[int] = None
+    ) -> List[Dict[str, Any]]:
+        """Find files by tag name.
+
+        DEPRECATED: Use NextcloudClient.find_files_by_tag() instead, which uses
+        the proper OCS Tags API rather than WebDAV SEARCH.
+
+        Args:
+            tag_name: Tag to filter by (e.g., "vector-index")
+            scope: Directory path to search in (empty string for user root)
+            limit: Maximum number of results to return
+
+        Returns:
+            List of files/directories with the specified tag
+
+        Examples:
+            # Find all files tagged with "vector-index"
+            results = await find_by_tag("vector-index")
+
+            # Find tagged files in a specific folder
+            results = await find_by_tag("vector-index", scope="Documents")
+        """
+        # Use LIKE for tag matching since tags can be comma-separated
+        where_conditions = f"""
+            <d:like>
+                <d:prop>
+                    <oc:tags/>
+                </d:prop>
+                <d:literal>%{tag_name}%</d:literal>
+            </d:like>
+        """
+
+        # Request tag property along with standard properties
+        properties = [
+            "displayname",
+            "getcontentlength",
+            "getcontenttype",
+            "getlastmodified",
+            "resourcetype",
+            "getetag",
+            "fileid",
+            "tags",
+        ]
+
+        return await self.search_files(
+            scope=scope,
+            where_conditions=where_conditions,
+            properties=properties,
+            limit=limit,
+        )
+
+    async def _get_file_info_by_id(self, file_id: int) -> Dict[str, Any]:
+        """Get file information by Nextcloud file ID using WebDAV.
+
+        Args:
+            file_id: Nextcloud internal file ID
+
+        Returns:
+            File information dictionary with path, size, content_type, etc.
+
+        Raises:
+            HTTPStatusError: If file not found or request fails
+        """
+        # Nextcloud allows accessing files by ID via special meta endpoint
+        meta_path = f"/remote.php/dav/meta/{file_id}/"
+
+        propfind_body = """<?xml version="1.0"?>
+        <d:propfind xmlns:d="DAV:" xmlns:oc="http://owncloud.org/ns">
+            <d:prop>
+                <d:displayname/>
+                <d:getcontentlength/>
+                <d:getcontenttype/>
+                <d:getlastmodified/>
+                <d:resourcetype/>
+                <d:getetag/>
+                <oc:fileid/>
+            </d:prop>
+        </d:propfind>"""
+
+        headers = {"Depth": "0", "Content-Type": "text/xml", "OCS-APIRequest": "true"}
+
+        response = await self._make_request(
+            "PROPFIND", meta_path, content=propfind_body, headers=headers
+        )
+        response.raise_for_status()
+
+        # Parse the XML response
+        root = ET.fromstring(response.content)
+        responses = root.findall(".//{DAV:}response")
+
+        if not responses:
+            raise RuntimeError(f"File ID {file_id} not found")
+
+        response_elem = responses[0]
+        href = response_elem.find(".//{DAV:}href")
+        if href is None:
+            raise RuntimeError(f"No href in response for file ID {file_id}")
+
+        propstat = response_elem.find(".//{DAV:}propstat")
+        if propstat is None:
+            raise RuntimeError(f"No propstat for file ID {file_id}")
+
+        prop = propstat.find(".//{DAV:}prop")
+        if prop is None:
+            raise RuntimeError(f"No prop for file ID {file_id}")
+
+        # Extract file path from displayname or construct from file ID
+        displayname_elem = prop.find(".//{DAV:}displayname")
+        name = (
+            displayname_elem.text if displayname_elem is not None else f"file_{file_id}"
+        )
+
+        # Get file properties
+        size_elem = prop.find(".//{DAV:}getcontentlength")
+        size = int(size_elem.text) if size_elem is not None and size_elem.text else 0
+
+        content_type_elem = prop.find(".//{DAV:}getcontenttype")
+        content_type = content_type_elem.text if content_type_elem is not None else None
+
+        modified_elem = prop.find(".//{DAV:}getlastmodified")
+        modified = modified_elem.text if modified_elem is not None else None
+
+        etag_elem = prop.find(".//{DAV:}getetag")
+        etag = (
+            etag_elem.text.strip('"')
+            if etag_elem is not None and etag_elem.text
+            else None
+        )
+
+        # Check if it's a directory
+        resourcetype = prop.find(".//{DAV:}resourcetype")
+        is_directory = (
+            resourcetype is not None
+            and resourcetype.find(".//{DAV:}collection") is not None
+        )
+
+        # Try to get actual file path - meta endpoint doesn't give us the real path
+        # so we'll construct a reasonable path from the name
+        # The calling code in NextcloudClient will have the context to determine the actual path
+        file_info = {
+            "name": name,
+            "path": f"/{name}",  # Placeholder - caller should use WebDAV to get real path if needed
+            "size": size,
+            "content_type": content_type,
+            "last_modified": modified,
+            "etag": etag,
+            "is_directory": is_directory,
+            "file_id": file_id,
+        }
+
+        logger.debug(f"Retrieved file info for ID {file_id}: {name}")
+        return file_info
+
+    async def get_tag_by_name(self, tag_name: str) -> dict[str, Any] | None:
+        """Get a system tag by its name via WebDAV.
+
+        Args:
+            tag_name: Name of the tag to find (case-sensitive)
+
+        Returns:
+            Tag dictionary if found, None otherwise
+        """
+        # Use WebDAV PROPFIND to list all systemtags
+        propfind_body = """<?xml version="1.0"?>
+<d:propfind xmlns:d="DAV:" xmlns:oc="http://owncloud.org/ns">
+  <d:prop>
+    <oc:id/>
+    <oc:display-name/>
+    <oc:user-visible/>
+    <oc:user-assignable/>
+  </d:prop>
+</d:propfind>"""
+
+        response = await self._client.request(
+            "PROPFIND",
+            "/remote.php/dav/systemtags/",
+            headers={"Depth": "1"},
+            content=propfind_body,
+        )
+        response.raise_for_status()
+
+        # Parse XML response
+        root = ET.fromstring(response.content)
+        ns = {
+            "d": "DAV:",
+            "oc": "http://owncloud.org/ns",
+        }
+
+        for response_elem in root.findall("d:response", ns):
+            href = response_elem.find("d:href", ns)
+            if href is None or href.text == "/remote.php/dav/systemtags/":
+                # Skip the collection itself
+                continue
+
+            propstat = response_elem.find("d:propstat", ns)
+            if propstat is None:
+                continue
+
+            prop = propstat.find("d:prop", ns)
+            if prop is None:
+                continue
+
+            # Extract tag properties
+            tag_id_elem = prop.find("oc:id", ns)
+            display_name_elem = prop.find("oc:display-name", ns)
+            user_visible_elem = prop.find("oc:user-visible", ns)
+            user_assignable_elem = prop.find("oc:user-assignable", ns)
+
+            if display_name_elem is not None and display_name_elem.text == tag_name:
+                tag_info = {
+                    "id": int(tag_id_elem.text) if tag_id_elem is not None else None,
+                    "name": display_name_elem.text,
+                    "userVisible": user_visible_elem.text.lower() == "true"
+                    if user_visible_elem is not None
+                    else True,
+                    "userAssignable": user_assignable_elem.text.lower() == "true"
+                    if user_assignable_elem is not None
+                    else True,
+                }
+                logger.debug(f"Found tag '{tag_name}' with ID {tag_info['id']}")
+                return tag_info
+
+        logger.debug(f"Tag '{tag_name}' not found")
+        return None
+
+    async def get_files_by_tag(self, tag_id: int) -> list[dict[str, Any]]:
+        """Get all files tagged with a specific system tag via WebDAV REPORT.
+
+        Args:
+            tag_id: Numeric ID of the tag
+
+        Returns:
+            List of file info dictionaries with path, size, content_type, etc.
+        """
+        # Use WebDAV REPORT method with systemtag filter, requesting all properties
+        report_body = f"""<?xml version="1.0"?>
+<oc:filter-files xmlns:d="DAV:" xmlns:oc="http://owncloud.org/ns" xmlns:nc="http://nextcloud.org/ns">
+  <d:prop>
+    <oc:fileid/>
+    <d:displayname/>
+    <d:getcontentlength/>
+    <d:getcontenttype/>
+    <d:getlastmodified/>
+    <d:getetag/>
+  </d:prop>
+  <oc:filter-rules>
+    <oc:systemtag>{tag_id}</oc:systemtag>
+  </oc:filter-rules>
+</oc:filter-files>"""
+
+        response = await self._client.request(
+            "REPORT",
+            f"{self._get_webdav_base_path()}/",
+            content=report_body,
+        )
+        response.raise_for_status()
+
+        # Parse XML response
+        root = ET.fromstring(response.content)
+        ns = {
+            "d": "DAV:",
+            "oc": "http://owncloud.org/ns",
+        }
+
+        files = []
+        for response_elem in root.findall("d:response", ns):
+            # Extract href (file path)
+            href_elem = response_elem.find("d:href", ns)
+            if href_elem is None or not href_elem.text:
+                continue
+
+            propstat = response_elem.find("d:propstat", ns)
+            if propstat is None:
+                continue
+
+            prop = propstat.find("d:prop", ns)
+            if prop is None:
+                continue
+
+            # Extract all properties
+            fileid_elem = prop.find("oc:fileid", ns)
+            displayname_elem = prop.find("d:displayname", ns)
+            contentlength_elem = prop.find("d:getcontentlength", ns)
+            contenttype_elem = prop.find("d:getcontenttype", ns)
+            lastmodified_elem = prop.find("d:getlastmodified", ns)
+            etag_elem = prop.find("d:getetag", ns)
+
+            if fileid_elem is None or not fileid_elem.text:
+                continue
+
+            # Decode href path and extract the file path
+            from urllib.parse import unquote
+
+            href_path = unquote(href_elem.text)
+            # Remove WebDAV prefix to get user-relative path
+            webdav_prefix = f"/remote.php/dav/files/{self.username}/"
+            file_path = href_path.replace(webdav_prefix, "/")
+
+            # Parse last modified timestamp
+            last_modified_timestamp = None
+            if lastmodified_elem is not None and lastmodified_elem.text:
+                from email.utils import parsedate_to_datetime
+
+                try:
+                    dt = parsedate_to_datetime(lastmodified_elem.text)
+                    last_modified_timestamp = int(dt.timestamp())
+                except Exception:
+                    pass
+
+            file_info = {
+                "id": int(fileid_elem.text),
+                "path": file_path,
+                "name": displayname_elem.text
+                if displayname_elem is not None
+                else file_path.split("/")[-1],
+                "size": int(contentlength_elem.text)
+                if contentlength_elem is not None and contentlength_elem.text
+                else 0,
+                "content_type": contenttype_elem.text
+                if contenttype_elem is not None
+                else "",
+                "last_modified": lastmodified_elem.text
+                if lastmodified_elem is not None
+                else None,
+                "last_modified_timestamp": last_modified_timestamp,
+                "etag": etag_elem.text if etag_elem is not None else None,
+            }
+            files.append(file_info)
+
+        logger.debug(f"Found {len(files)} files with tag ID {tag_id}")
+        return files

nextcloud_mcp_server/config.py

@@ -2,8 +2,37 @@ import logging
 import logging.config
 import os
 from dataclasses import dataclass
+from enum import Enum
 from typing import Any, Optional
 
+
+class DeploymentMode(Enum):
+    """Deployment mode for the MCP server.
+
+    SELF_HOSTED: Full features, environment-based configuration.
+                 Supports vector sync, semantic search, admin UI.
+
+    SMITHERY_STATELESS: Stateless mode for Smithery hosting.
+                        Session-based configuration, no persistent storage.
+                        Excludes semantic search, vector sync, admin UI.
+    """
+
+    SELF_HOSTED = "self_hosted"
+    SMITHERY_STATELESS = "smithery"
+
+
+def get_deployment_mode() -> DeploymentMode:
+    """Detect deployment mode from environment.
+
+    Returns:
+        DeploymentMode.SMITHERY_STATELESS if SMITHERY_DEPLOYMENT=true,
+        otherwise DeploymentMode.SELF_HOSTED (default).
+    """
+    if os.getenv("SMITHERY_DEPLOYMENT", "false").lower() == "true":
+        return DeploymentMode.SMITHERY_STATELESS
+    return DeploymentMode.SELF_HOSTED
+
+
 LOGGING_CONFIG = {
     "version": 1,
     "disable_existing_loggers": False,
@@ -102,6 +131,14 @@ def get_document_processor_config() -> dict[str, Any]:
             "lang": os.getenv("TESSERACT_LANG", "eng"),
         }
 
+    # PyMuPDF configuration (local PDF processing)
+    if os.getenv("ENABLE_PYMUPDF", "true").lower() == "true":  # Enabled by default
+        config["processors"]["pymupdf"] = {
+            "extract_images": os.getenv("PYMUPDF_EXTRACT_IMAGES", "true").lower()
+            == "true",
+            "image_dir": os.getenv("PYMUPDF_IMAGE_DIR"),  # None = use temp directory
+        }
+
     # Custom processor (via HTTP API)
     if os.getenv("ENABLE_CUSTOM_PROCESSOR", "false").lower() == "true":
         custom_url = os.getenv("CUSTOM_PROCESSOR_URL")

nextcloud_mcp_server/context.py

@@ -1,21 +1,37 @@
 """Helper functions for accessing context in MCP tools."""
 
+import logging
+
+from httpx import BasicAuth
 from mcp.server.fastmcp import Context
 
 from nextcloud_mcp_server.client import NextcloudClient
-from nextcloud_mcp_server.config import get_settings
+from nextcloud_mcp_server.config import (
+    DeploymentMode,
+    get_deployment_mode,
+    get_settings,
+)
+
+logger = logging.getLogger(__name__)
 
 
 async def get_client(ctx: Context) -> NextcloudClient:
     """
     Get the appropriate Nextcloud client based on authentication mode.
 
-    ADR-005 compliant implementation supporting two modes:
-    1. BasicAuth mode: Returns shared client from lifespan context
-    2. Multi-audience mode (ENABLE_TOKEN_EXCHANGE=false, default):
-       Token already contains both MCP and Nextcloud audiences - use directly
-    3. Token exchange mode (ENABLE_TOKEN_EXCHANGE=true):
-       Exchange MCP token for Nextcloud token via RFC 8693
+    ADR-016 compliant implementation supporting three deployment modes:
+
+    1. Smithery stateless mode (SMITHERY_DEPLOYMENT=true):
+       Create client from session configuration (nextcloud_url, username, app_password)
+       No persistent state - client created per-request from Smithery session config.
+
+    2. BasicAuth mode: Returns shared client from lifespan context
+
+    3. OAuth mode:
+       a. Multi-audience mode (ENABLE_TOKEN_EXCHANGE=false, default):
+          Token already contains both MCP and Nextcloud audiences - use directly
+       b. Token exchange mode (ENABLE_TOKEN_EXCHANGE=true):
+          Exchange MCP token for Nextcloud token via RFC 8693
 
     SECURITY: Token passthrough has been REMOVED. All OAuth modes validate
     proper token audiences per MCP Security Best Practices specification.
@@ -24,7 +40,7 @@ async def get_client(ctx: Context) -> NextcloudClient:
     by the MCP server via @require_scopes decorator, not by the IdP.
 
     This function automatically detects the authentication mode by checking
-    the type of the lifespan context.
+    the deployment mode and type of the lifespan context.
 
     Args:
         ctx: MCP request context
@@ -34,6 +50,7 @@ async def get_client(ctx: Context) -> NextcloudClient:
 
     Raises:
         AttributeError: If context doesn't contain expected data
+        ValueError: If Smithery mode but session config is missing required fields
 
     Example:
         ```python
@@ -43,6 +60,12 @@ async def get_client(ctx: Context) -> NextcloudClient:
             return await client.capabilities()
         ```
     """
+    deployment_mode = get_deployment_mode()
+
+    # ADR-016: Smithery stateless mode - create client from session config
+    if deployment_mode == DeploymentMode.SMITHERY_STATELESS:
+        return _get_client_from_session_config(ctx)
+
     settings = get_settings()
     lifespan_ctx = ctx.request_context.lifespan_context
 
@@ -75,3 +98,82 @@ async def get_client(ctx: Context) -> NextcloudClient:
         f"Lifespan context does not have 'client' or 'nextcloud_host' attribute. "
         f"Type: {type(lifespan_ctx)}"
     )
+
+
+def _get_client_from_session_config(ctx: Context) -> NextcloudClient:
+    """
+    Create NextcloudClient from Smithery session configuration.
+
+    ADR-016: In Smithery stateless mode, each request includes session config
+    with the user's Nextcloud credentials. This function creates a fresh client
+    for each request - no state is persisted between requests.
+
+    For container runtime, config is extracted from URL query parameters by
+    SmitheryConfigMiddleware and stored in a context variable.
+
+    Expected session config fields (from Smithery configSchema):
+    - nextcloud_url: str - Nextcloud instance URL (required)
+    - username: str - Nextcloud username (required)
+    - app_password: str - Nextcloud app password (required)
+
+    Args:
+        ctx: MCP request context (not used directly for Smithery config)
+
+    Returns:
+        NextcloudClient configured with session credentials
+
+    Raises:
+        ValueError: If required session config fields are missing
+    """
+    # ADR-016: Get session config from context variable (set by SmitheryConfigMiddleware)
+    from nextcloud_mcp_server.app import get_smithery_session_config
+
+    session_config = get_smithery_session_config()
+
+    if session_config is None:
+        raise ValueError(
+            "Session configuration required in Smithery mode. "
+            "Ensure nextcloud_url, username, and app_password are provided as URL query parameters."
+        )
+
+    # Extract required fields - config is always a dict from SmitheryConfigMiddleware
+    nextcloud_url = session_config.get("nextcloud_url")
+    username = session_config.get("username")
+    app_password = session_config.get("app_password")
+
+    # Validate required fields
+    missing_fields = []
+    if not nextcloud_url:
+        missing_fields.append("nextcloud_url")
+    if not username:
+        missing_fields.append("username")
+    if not app_password:
+        missing_fields.append("app_password")
+
+    if missing_fields:
+        raise ValueError(
+            f"Missing required session config fields: {', '.join(missing_fields)}. "
+            f"Configure these in the Smithery connection settings."
+        )
+
+    # Type assertions after validation (for type checker)
+    # These are guaranteed to be str after the missing_fields check above
+    assert nextcloud_url is not None
+    assert username is not None
+    assert app_password is not None
+
+    # Validate URL format
+    if not nextcloud_url.startswith(("http://", "https://")):
+        raise ValueError(
+            f"Invalid nextcloud_url: {nextcloud_url}. "
+            f"Must start with http:// or https://"
+        )
+
+    logger.debug(f"Creating Smithery client for {nextcloud_url} as {username}")
+
+    # Create client with session credentials using BasicAuth
+    return NextcloudClient(
+        base_url=nextcloud_url,
+        username=username,
+        auth=BasicAuth(username, app_password),
+    )

nextcloud_mcp_server/document_processors/__init__.py

@@ -1,12 +1,18 @@
 """Document processing plugins for extracting text from various file formats."""
 
 from .base import DocumentProcessor, ProcessingResult, ProcessorError
+from .pymupdf import PyMuPDFProcessor
 from .registry import ProcessorRegistry, get_registry
 
+# Register processors at module initialization
+_registry = get_registry()
+_registry.register(PyMuPDFProcessor(), priority=10)
+
 __all__ = [
     "DocumentProcessor",
     "ProcessingResult",
     "ProcessorError",
     "ProcessorRegistry",
     "get_registry",
+    "PyMuPDFProcessor",
 ]

nextcloud_mcp_server/document_processors/pymupdf.py

@@ -0,0 +1,253 @@
+"""Document processor using PyMuPDF (fitz) library."""
+
+import logging
+import pathlib
+import tempfile
+from collections.abc import Awaitable, Callable
+from typing import Any, Optional
+
+# NOTE: Do NOT call pymupdf.layout.activate() here!
+# It changes the behavior of pymupdf4llm.to_markdown() when page_chunks=True,
+# causing it to return a string instead of a list[dict].
+# See: https://github.com/pymupdf/pymupdf4llm/issues/323
+import pymupdf
+import pymupdf4llm
+
+from .base import DocumentProcessor, ProcessingResult, ProcessorError
+
+logger = logging.getLogger(__name__)
+
+
+class PyMuPDFProcessor(DocumentProcessor):
+    """Document processor using PyMuPDF library for PDF processing.
+
+    PyMuPDF (fitz) is a fast, local PDF processing library that extracts text,
+    metadata, and images without requiring external API calls.
+
+    Features:
+    - Fast text extraction with layout preservation
+    - PDF metadata extraction (title, author, creation date, page count)
+    - Image extraction for future multimodal support
+    - Page number tracking for precise citations
+    """
+
+    SUPPORTED_TYPES = {
+        "application/pdf",
+    }
+
+    def __init__(
+        self,
+        extract_images: bool = True,
+        image_dir: Optional[str | pathlib.Path] = None,
+    ):
+        """Initialize PyMuPDF processor.
+
+        Args:
+            extract_images: Whether to extract embedded images from PDFs
+            image_dir: Directory to store extracted images (defaults to temp directory)
+        """
+        self.extract_images = extract_images
+
+        if image_dir is None:
+            self.image_dir = pathlib.Path(tempfile.gettempdir()) / "pdf-images"
+        else:
+            self.image_dir = pathlib.Path(image_dir)
+
+        # Create image directory if it doesn't exist
+        if self.extract_images:
+            self.image_dir.mkdir(exist_ok=True, parents=True)
+            logger.info(
+                f"Initialized PyMuPDFProcessor with image extraction to {self.image_dir}"
+            )
+        else:
+            logger.info("Initialized PyMuPDFProcessor without image extraction")
+
+    @property
+    def name(self) -> str:
+        return "pymupdf"
+
+    @property
+    def supported_mime_types(self) -> set[str]:
+        return self.SUPPORTED_TYPES
+
+    async def process(
+        self,
+        content: bytes,
+        content_type: str,
+        filename: Optional[str] = None,
+        options: Optional[dict[str, Any]] = None,
+        progress_callback: Optional[
+            Callable[[float, Optional[float], Optional[str]], Awaitable[None]]
+        ] = None,
+    ) -> ProcessingResult:
+        """Process a PDF document and extract text, metadata, and images.
+
+        Args:
+            content: PDF document bytes
+            content_type: MIME type (should be application/pdf)
+            filename: Optional filename for better error messages
+            options: Processing options (currently unused)
+            progress_callback: Optional callback for progress updates
+
+        Returns:
+            ProcessingResult with extracted text and metadata
+
+        Raises:
+            ProcessorError: If PDF processing fails
+        """
+        import anyio
+
+        try:
+            if progress_callback:
+                await progress_callback(0, 100, "Opening PDF document")
+
+            # Open document and extract metadata in thread
+            doc = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+                lambda: pymupdf.open("pdf", content)
+            )
+
+            metadata = self._extract_metadata(doc, filename)
+            metadata["file_size"] = len(content)
+            page_count = doc.page_count
+
+            if progress_callback:
+                await progress_callback(10, 100, f"Extracting {page_count} pages")
+
+            # Prepare image directory if needed
+            pdf_image_dir = None
+            if self.extract_images:
+                pdf_id = filename.replace("/", "_") if filename else "unknown"
+                pdf_image_dir = self.image_dir / pdf_id
+                pdf_image_dir.mkdir(exist_ok=True, parents=True)
+
+            # Extract all pages in a single call with page_chunks=True
+            def do_extract() -> list[dict[str, Any]]:
+                # When page_chunks=True, to_markdown returns list[dict] not str
+                return pymupdf4llm.to_markdown(  # type: ignore[return-value]
+                    doc,
+                    write_images=self.extract_images,
+                    image_path=pdf_image_dir if self.extract_images else None,
+                    page_chunks=True,
+                )
+
+            page_chunks: list[dict[str, Any]] = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+                do_extract
+            )
+
+            if progress_callback:
+                await progress_callback(90, 100, "Building result")
+
+            # Extract page texts and build boundaries from chunks
+            page_texts: list[str] = []
+            page_boundaries: list[dict[str, Any]] = []
+            current_offset = 0
+            for chunk in page_chunks:
+                text = chunk.get("text", "")
+                page_num = chunk.get("metadata", {}).get("page", len(page_texts) + 1)
+                page_texts.append(text)
+                page_boundaries.append(
+                    {
+                        "page": page_num,
+                        "start_offset": current_offset,
+                        "end_offset": current_offset + len(text),
+                    }
+                )
+                current_offset += len(text)
+
+            # Collect image paths
+            image_paths = []
+            if pdf_image_dir and pdf_image_dir.exists():
+                image_paths = [str(p) for p in pdf_image_dir.glob("*")]
+
+            # Build final text and metadata
+            md_text = "".join(page_texts)
+            metadata["has_images"] = len(image_paths) > 0
+            if image_paths:
+                metadata["image_count"] = len(image_paths)
+                metadata["image_paths"] = image_paths
+            metadata["page_boundaries"] = page_boundaries
+
+            # Close document
+            doc.close()
+
+            if progress_callback:
+                await progress_callback(100, 100, "Processing complete")
+
+            logger.info(
+                f"Successfully processed PDF {filename or '<bytes>'}: "
+                f"{metadata['page_count']} pages, {len(md_text)} chars, "
+                f"{metadata.get('image_count', 0)} images"
+            )
+
+            return ProcessingResult(
+                text=md_text,
+                metadata=metadata,
+                processor=self.name,
+                success=True,
+            )
+
+        except Exception as e:
+            error_msg = f"Failed to process PDF {filename or '<bytes>'}: {e}"
+            logger.error(error_msg, exc_info=True)
+            raise ProcessorError(error_msg) from e
+
+    def _extract_metadata(
+        self, doc: pymupdf.Document, filename: Optional[str]
+    ) -> dict[str, Any]:
+        """Extract metadata from PDF document.
+
+        Args:
+            doc: Opened PyMuPDF document
+            filename: Optional filename
+
+        Returns:
+            Dictionary with PDF metadata
+        """
+        metadata: dict[str, Any] = {}
+
+        # Basic document info
+        metadata["page_count"] = doc.page_count
+        metadata["format"] = "PDF 1." + str(
+            doc.pdf_version() if hasattr(doc, "pdf_version") else "?"  # type: ignore[call-non-callable]
+        )
+
+        if filename:
+            metadata["filename"] = filename
+
+        # Extract PDF metadata dictionary
+        pdf_metadata = doc.metadata
+        if pdf_metadata:
+            # Standard PDF metadata fields
+            if pdf_metadata.get("title"):
+                metadata["title"] = pdf_metadata["title"]
+            if pdf_metadata.get("author"):
+                metadata["author"] = pdf_metadata["author"]
+            if pdf_metadata.get("subject"):
+                metadata["subject"] = pdf_metadata["subject"]
+            if pdf_metadata.get("keywords"):
+                metadata["keywords"] = pdf_metadata["keywords"]
+            if pdf_metadata.get("creator"):
+                metadata["creator"] = pdf_metadata["creator"]
+            if pdf_metadata.get("producer"):
+                metadata["producer"] = pdf_metadata["producer"]
+            if pdf_metadata.get("creationDate"):
+                metadata["creation_date"] = pdf_metadata["creationDate"]
+            if pdf_metadata.get("modDate"):
+                metadata["modification_date"] = pdf_metadata["modDate"]
+
+        return metadata
+
+    async def health_check(self) -> bool:
+        """Check if PyMuPDF is available and working.
+
+        Returns:
+            True if processor is ready to use
+        """
+        try:
+            # Try to create a simple PDF in memory
+            test_doc = pymupdf.open()
+            test_doc.close()
+            return True
+        except Exception as e:
+            logger.error(f"PyMuPDF health check failed: {e}")
+            return False

nextcloud_mcp_server/embedding/bm25_provider.py

@@ -37,7 +37,9 @@ class BM25SparseEmbeddingProvider:
 
     def encode(self, text: str) -> dict[str, Any]:
         """
-        Generate BM25 sparse embedding for a single text.
+        Generate BM25 sparse embedding for a single text (synchronous).
+
+        Note: For async contexts, prefer encode_async() to avoid blocking the event loop.
 
         Args:
             text: Input text to encode
@@ -53,7 +55,24 @@ class BM25SparseEmbeddingProvider:
             "values": sparse_embedding.values.tolist(),
         }
 
-    def encode_batch(self, texts: list[str]) -> list[dict[str, Any]]:
+    async def encode_async(self, text: str) -> dict[str, Any]:
+        """
+        Generate BM25 sparse embedding for a single text (async).
+
+        Runs CPU-bound BM25 encoding in thread pool to avoid blocking the event loop.
+
+        Args:
+            text: Input text to encode
+
+        Returns:
+            Dictionary with 'indices' and 'values' keys for Qdrant sparse vector
+        """
+        import anyio
+
+        # Run CPU-bound BM25 encoding in thread pool
+        return await anyio.to_thread.run_sync(lambda: self.encode(text))  # type: ignore[attr-defined]
+
+    async def encode_batch(self, texts: list[str]) -> list[dict[str, Any]]:
         """
         Generate BM25 sparse embeddings for multiple texts (batched).
 
@@ -63,7 +82,12 @@ class BM25SparseEmbeddingProvider:
         Returns:
             List of dictionaries with 'indices' and 'values' for each text
         """
-        sparse_embeddings = list(self.model.embed(texts))
+        import anyio
+
+        # Run CPU-bound BM25 encoding in thread pool to avoid blocking event loop
+        sparse_embeddings = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+            lambda: list(self.model.embed(texts))
+        )
 
         return [
             {

nextcloud_mcp_server/models/semantic.py

@@ -10,7 +10,7 @@ from .base import BaseResponse
 class SemanticSearchResult(BaseModel):
     """Model for semantic search results with additional metadata."""
 
-    id: int = Field(description="Document ID")
+    id: int = Field(description="Document ID (int for all document types)")
     doc_type: str = Field(
         description="Document type (note, calendar_event, deck_card, etc.)"
     )
@@ -35,6 +35,29 @@ class SemanticSearchResult(BaseModel):
     chunk_end_offset: Optional[int] = Field(
         default=None, description="Character position where chunk ends in document"
     )
+    page_number: Optional[int] = Field(
+        default=None, description="Page number for PDF documents"
+    )
+    # Context expansion fields (optional, populated when include_context=True)
+    has_context_expansion: bool = Field(
+        default=False, description="Whether context expansion was performed"
+    )
+    marked_text: Optional[str] = Field(
+        default=None,
+        description="Full text with position markers around matched chunk",
+    )
+    before_context: Optional[str] = Field(
+        default=None, description="Text before the matched chunk"
+    )
+    after_context: Optional[str] = Field(
+        default=None, description="Text after the matched chunk"
+    )
+    has_before_truncation: Optional[bool] = Field(
+        default=None, description="Whether before_context was truncated"
+    )
+    has_after_truncation: Optional[bool] = Field(
+        default=None, description="Whether after_context was truncated"
+    )
 
 
 class SemanticSearchResponse(BaseResponse):

nextcloud_mcp_server/observability/logging_config.py

@@ -37,7 +37,7 @@ class HealthCheckFilter(logging.Filter):
         """
         # Check if the log message contains health check endpoints
         message = record.getMessage()
-        return not any(
+        health_check = any(
             endpoint in message
             for endpoint in [
                 "/health/live",
@@ -47,6 +47,8 @@ class HealthCheckFilter(logging.Filter):
             ]
         )
 
+        return not health_check
+
 
 class TraceContextFormatter(JsonFormatter):
     """

nextcloud_mcp_server/providers/ollama.py

@@ -92,14 +92,21 @@ class OllamaProvider(Provider):
         response.raise_for_status()
         return response.json()["embedding"]
 
-    async def embed_batch(self, texts: list[str]) -> list[list[float]]:
+    async def embed_batch(
+        self, texts: list[str], batch_size: int = 32
+    ) -> list[list[float]]:
         """
-        Generate embeddings for multiple texts (batched requests).
+        Generate embeddings for multiple texts using Ollama's batch API.
 
-        Note: Ollama doesn't have native batch API, so we send requests sequentially.
+        Uses /api/embed endpoint with array input for efficient batch processing.
+        Conservative batch size (32) prevents quality degradation observed in
+        Ollama issue #6262 with larger batches.
+
+        Note: Ollama processes batches serially, not in parallel.
 
         Args:
             texts: List of texts to embed
+            batch_size: Maximum texts per batch (default: 32)
 
         Returns:
             List of vector embeddings
@@ -112,11 +119,17 @@ class OllamaProvider(Provider):
                 "Embedding not supported - no embedding_model configured"
             )
 
-        embeddings = []
-        for text in texts:
-            embedding = await self.embed(text)
-            embeddings.append(embedding)
-        return embeddings
+        all_embeddings = []
+        for i in range(0, len(texts), batch_size):
+            batch = texts[i : i + batch_size]
+            response = await self.client.post(
+                f"{self.base_url}/api/embed",
+                json={"model": self.embedding_model, "input": batch},
+            )
+            response.raise_for_status()
+            all_embeddings.extend(response.json()["embeddings"])
+
+        return all_embeddings
 
     async def _detect_dimension(self):
         """

nextcloud_mcp_server/search/algorithms.py

@@ -83,6 +83,7 @@ async def get_indexed_doc_types(user_id: str) -> set[str]:
     from qdrant_client.models import FieldCondition, Filter, MatchValue
 
     from nextcloud_mcp_server.config import get_settings
+    from nextcloud_mcp_server.vector.placeholder import get_placeholder_filter
     from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
     logger = logging.getLogger(__name__)
@@ -97,7 +98,10 @@ async def get_indexed_doc_types(user_id: str) -> set[str]:
         scroll_results, _next_offset = await qdrant_client.scroll(
             collection_name=collection,
             scroll_filter=Filter(
-                must=[FieldCondition(key="user_id", match=MatchValue(value=user_id))]
+                must=[
+                    get_placeholder_filter(),  # Exclude placeholders from doc_type discovery
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                ]
             ),
             limit=1000,  # Sample size to discover types
             with_payload=["doc_type"],
@@ -123,7 +127,7 @@ class SearchResult:
     """A single search result with metadata and score.
 
     Attributes:
-        id: Document ID
+        id: Document ID (int for all document types)
         doc_type: Document type (note, file, calendar, contact, etc.)
         title: Document title
         excerpt: Content excerpt showing match context
@@ -133,6 +137,10 @@ class SearchResult:
         metadata: Additional algorithm-specific metadata
         chunk_start_offset: Character position where chunk starts (None if not available)
         chunk_end_offset: Character position where chunk ends (None if not available)
+        page_number: Page number for PDF documents (None for other doc types)
+        chunk_index: Zero-based index of this chunk in the document
+        total_chunks: Total number of chunks in the document
+        point_id: Qdrant point ID for batch vector retrieval (None if not from Qdrant)
     """
 
     id: int
@@ -143,6 +151,10 @@ class SearchResult:
     metadata: dict[str, Any] | None = None
     chunk_start_offset: int | None = None
     chunk_end_offset: int | None = None
+    page_number: int | None = None
+    chunk_index: int = 0
+    total_chunks: int = 1
+    point_id: str | None = None
 
     def __post_init__(self):
         """Validate score is non-negative.
@@ -162,8 +174,15 @@ class SearchAlgorithm(ABC):
 
     All search algorithms must implement the search() method with consistent
     interface, allowing them to be used interchangeably.
+
+    Attributes:
+        query_embedding: The query embedding generated during the last search.
+            Available after search() completes for algorithms that use embeddings.
+            Can be reused by callers to avoid redundant embedding generation.
     """
 
+    query_embedding: list[float] | None = None
+
     @abstractmethod
     async def search(
         self,

nextcloud_mcp_server/search/bm25_hybrid.py

@@ -10,6 +10,7 @@ from nextcloud_mcp_server.config import get_settings
 from nextcloud_mcp_server.embedding import get_bm25_service, get_embedding_service
 from nextcloud_mcp_server.observability.metrics import record_qdrant_operation
 from nextcloud_mcp_server.search.algorithms import SearchAlgorithm, SearchResult
+from nextcloud_mcp_server.vector.placeholder import get_placeholder_filter
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
 logger = logging.getLogger(__name__)
@@ -72,6 +73,9 @@ class BM25HybridSearchAlgorithm(SearchAlgorithm):
         Returns unverified results from Qdrant. Access verification should be
         performed separately at the final output stage using verify_search_results().
 
+        Deduplicates by (doc_id, doc_type, chunk_start_offset, chunk_end_offset)
+        to show multiple chunks from the same document while avoiding duplicate chunks.
+
         Args:
             query: Natural language or keyword search query
             user_id: User ID for filtering
@@ -97,11 +101,13 @@ class BM25HybridSearchAlgorithm(SearchAlgorithm):
         # Generate dense embedding for semantic search
         embedding_service = get_embedding_service()
         dense_embedding = await embedding_service.embed(query)
+        # Store for reuse by callers (e.g., viz_routes PCA visualization)
+        self.query_embedding = dense_embedding
         logger.debug(f"Generated dense embedding (dimension={len(dense_embedding)})")
 
         # Generate sparse embedding for BM25 keyword search
         bm25_service = get_bm25_service()
-        sparse_embedding = bm25_service.encode(query)
+        sparse_embedding = await bm25_service.encode_async(query)
         logger.debug(
             f"Generated sparse embedding "
             f"({len(sparse_embedding['indices'])} non-zero terms)"
@@ -109,10 +115,11 @@ class BM25HybridSearchAlgorithm(SearchAlgorithm):
 
         # Build Qdrant filter
         filter_conditions = [
+            get_placeholder_filter(),  # Always exclude placeholders from user-facing queries
             FieldCondition(
                 key="user_id",
                 match=MatchValue(value=user_id),
-            )
+            ),
         ]
 
         # Add doc_type filter if specified
@@ -176,20 +183,24 @@ class BM25HybridSearchAlgorithm(SearchAlgorithm):
                 f"Top 3 {self.fusion_name.upper()} fusion scores: {top_scores}"
             )
 
-        # Deduplicate by (doc_id, doc_type) - multiple chunks per document
-        seen_docs = set()
+        # Deduplicate by (doc_id, doc_type, chunk_start, chunk_end)
+        # This allows multiple chunks from same doc, but removes duplicate chunks
+        seen_chunks = set()
         results = []
 
         for result in search_response.points:
-            doc_id = int(result.payload["doc_id"])
+            # doc_id can be int (notes) or str (files - file paths)
+            doc_id = result.payload["doc_id"]
             doc_type = result.payload.get("doc_type", "note")
-            doc_key = (doc_id, doc_type)
+            chunk_start = result.payload.get("chunk_start_offset")
+            chunk_end = result.payload.get("chunk_end_offset")
+            chunk_key = (doc_id, doc_type, chunk_start, chunk_end)
 
-            # Skip if we've already seen this document
-            if doc_key in seen_docs:
+            # Skip if we've already seen this exact chunk
+            if chunk_key in seen_chunks:
                 continue
 
-            seen_docs.add(doc_key)
+            seen_chunks.add(chunk_key)
 
             # Return unverified results (verification happens at output stage)
             results.append(
@@ -206,6 +217,10 @@ class BM25HybridSearchAlgorithm(SearchAlgorithm):
                     },
                     chunk_start_offset=result.payload.get("chunk_start_offset"),
                     chunk_end_offset=result.payload.get("chunk_end_offset"),
+                    page_number=result.payload.get("page_number"),
+                    chunk_index=result.payload.get("chunk_index", 0),
+                    total_chunks=result.payload.get("total_chunks", 1),
+                    point_id=str(result.id),  # Qdrant point ID for batch retrieval
                 )
             )
 

nextcloud_mcp_server/search/context.py

@@ -0,0 +1,598 @@
+"""Context expansion for search results.
+
+Provides utilities to expand matched chunks with surrounding context and
+position markers for better visualization and understanding of search results.
+"""
+
+import logging
+from dataclasses import dataclass
+
+from nextcloud_mcp_server.client import NextcloudClient
+
+logger = logging.getLogger(__name__)
+
+
+async def _get_chunk_from_qdrant(
+    user_id: str, doc_id: int, doc_type: str, chunk_start: int, chunk_end: int
+) -> str | None:
+    """Retrieve full chunk text from Qdrant payload.
+
+    This avoids re-fetching and re-parsing documents by using the cached
+    chunk content already stored in Qdrant.
+
+    Args:
+        user_id: User ID who owns the document
+        doc_id: Document ID
+        doc_type: Document type (e.g., "note", "file")
+        chunk_start: Character offset where chunk starts
+        chunk_end: Character offset where chunk ends
+
+    Returns:
+        Full chunk text from Qdrant excerpt field, or None if not found
+    """
+    try:
+        from qdrant_client.models import FieldCondition, Filter, MatchValue
+
+        from nextcloud_mcp_server.config import get_settings
+        from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
+
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Query for the specific chunk
+        scroll_result = await qdrant_client.scroll(
+            collection_name=settings.get_collection_name(),
+            scroll_filter=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=doc_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value=doc_type)),
+                    FieldCondition(
+                        key="chunk_start_offset", match=MatchValue(value=chunk_start)
+                    ),
+                    FieldCondition(
+                        key="chunk_end_offset", match=MatchValue(value=chunk_end)
+                    ),
+                ]
+            ),
+            limit=1,
+            with_payload=["excerpt"],
+            with_vectors=False,
+        )
+
+        if scroll_result[0]:
+            point = scroll_result[0][0]
+            excerpt = point.payload.get("excerpt")
+            if excerpt:
+                logger.debug(
+                    f"Retrieved chunk from Qdrant for {doc_type} {doc_id}: "
+                    f"{len(excerpt)} chars"
+                )
+                return str(excerpt)
+
+        logger.debug(
+            f"Chunk not found in Qdrant for {doc_type} {doc_id}, "
+            f"chunk [{chunk_start}:{chunk_end}]. Will fall back to document fetch."
+        )
+        return None
+
+    except Exception as e:
+        logger.error(
+            f"Error querying Qdrant for chunk: {e}. Falling back to document fetch.",
+            exc_info=True,
+        )
+        return None
+
+
+async def _get_chunk_by_index_from_qdrant(
+    user_id: str, doc_id: int, doc_type: str, chunk_index: int
+) -> str | None:
+    """Retrieve chunk text by chunk_index from Qdrant payload.
+
+    Used to fetch adjacent chunks for context expansion.
+
+    Args:
+        user_id: User ID who owns the document
+        doc_id: Document ID
+        doc_type: Document type (e.g., "note", "file")
+        chunk_index: Zero-based chunk index in document
+
+    Returns:
+        Full chunk text from Qdrant excerpt field, or None if not found
+    """
+    try:
+        from qdrant_client.models import FieldCondition, Filter, MatchValue
+
+        from nextcloud_mcp_server.config import get_settings
+        from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
+
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Query for chunk by index
+        scroll_result = await qdrant_client.scroll(
+            collection_name=settings.get_collection_name(),
+            scroll_filter=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=doc_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value=doc_type)),
+                    FieldCondition(
+                        key="chunk_index", match=MatchValue(value=chunk_index)
+                    ),
+                ]
+            ),
+            limit=1,
+            with_payload=["excerpt"],
+            with_vectors=False,
+        )
+
+        if scroll_result[0]:
+            point = scroll_result[0][0]
+            excerpt = point.payload.get("excerpt")
+            if excerpt:
+                logger.debug(
+                    f"Retrieved adjacent chunk {chunk_index} from Qdrant for "
+                    f"{doc_type} {doc_id}: {len(excerpt)} chars"
+                )
+                return str(excerpt)
+
+        return None
+
+    except Exception as e:
+        logger.debug(
+            f"Could not retrieve adjacent chunk {chunk_index} for "
+            f"{doc_type} {doc_id}: {e}"
+        )
+        return None
+
+
+async def _get_file_path_from_qdrant(
+    user_id: str, file_id: int, chunk_start: int, chunk_end: int
+) -> str | None:
+    """Resolve file_id to file_path by querying Qdrant payload.
+
+    Args:
+        user_id: User ID who owns the file
+        file_id: Numeric file ID
+        chunk_start: Character offset where chunk starts
+        chunk_end: Character offset where chunk ends
+
+    Returns:
+        File path string, or None if not found in Qdrant
+    """
+    try:
+        from qdrant_client.models import FieldCondition, Filter, MatchValue
+
+        from nextcloud_mcp_server.config import get_settings
+        from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
+
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Query for the specific chunk
+        scroll_result = await qdrant_client.scroll(
+            collection_name=settings.get_collection_name(),
+            scroll_filter=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=file_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value="file")),
+                    FieldCondition(
+                        key="chunk_start_offset", match=MatchValue(value=chunk_start)
+                    ),
+                    FieldCondition(
+                        key="chunk_end_offset", match=MatchValue(value=chunk_end)
+                    ),
+                ]
+            ),
+            limit=1,
+            with_payload=["file_path"],
+            with_vectors=False,
+        )
+
+        if scroll_result[0]:
+            point = scroll_result[0][0]
+            file_path = point.payload.get("file_path")
+            if file_path:
+                logger.debug(f"Resolved file_id {file_id} to file_path {file_path}")
+                return str(file_path)
+
+        logger.warning(
+            f"Could not find file_path in Qdrant for file_id {file_id}, "
+            f"chunk [{chunk_start}:{chunk_end}]"
+        )
+        return None
+
+    except Exception as e:
+        logger.error(f"Error querying Qdrant for file_path: {e}", exc_info=True)
+        return None
+
+
+@dataclass
+class ChunkContext:
+    """Expanded chunk with surrounding context and position markers.
+
+    Attributes:
+        chunk_text: The matched chunk text
+        before_context: Text before the chunk (up to context_chars)
+        after_context: Text after the chunk (up to context_chars)
+        chunk_start_offset: Character position where chunk starts in document
+        chunk_end_offset: Character position where chunk ends in document
+        page_number: Page number for PDFs (None for other doc types)
+        chunk_index: Zero-based chunk index (N in "chunk N of M")
+        total_chunks: Total number of chunks in document
+        marked_text: Full text with position markers around the chunk
+        has_before_truncation: True if before_context was truncated
+        has_after_truncation: True if after_context was truncated
+    """
+
+    chunk_text: str
+    before_context: str
+    after_context: str
+    chunk_start_offset: int
+    chunk_end_offset: int
+    page_number: int | None
+    chunk_index: int
+    total_chunks: int
+    marked_text: str
+    has_before_truncation: bool
+    has_after_truncation: bool
+
+
+async def get_chunk_with_context(
+    nc_client: NextcloudClient,
+    user_id: str,
+    doc_id: str | int,
+    doc_type: str,
+    chunk_start: int,
+    chunk_end: int,
+    page_number: int | None = None,
+    chunk_index: int = 0,
+    total_chunks: int = 1,
+    context_chars: int = 300,
+) -> ChunkContext | None:
+    """Fetch chunk with surrounding context.
+
+    First tries to retrieve the chunk from Qdrant (fast, cached). If that fails
+    (e.g., legacy data with truncated excerpts), falls back to fetching and
+    parsing the full document (slower, for PDFs especially).
+
+    Args:
+        nc_client: Authenticated Nextcloud client
+        user_id: User ID who owns the document
+        doc_id: Document ID (int for notes/files)
+        doc_type: Type of document ("note", "file", etc.)
+        chunk_start: Character offset where chunk starts
+        chunk_end: Character offset where chunk ends
+        page_number: Optional page number for PDFs
+        chunk_index: Zero-based chunk index in document
+        total_chunks: Total number of chunks in document
+        context_chars: Number of characters to include before/after chunk
+
+    Returns:
+        ChunkContext with expanded context and markers, or None if document
+        cannot be retrieved
+    """
+    # Convert doc_id to int for Qdrant query
+    doc_id_int = (
+        int(doc_id)
+        if isinstance(doc_id, str) and doc_id.isdigit()
+        else (doc_id if isinstance(doc_id, int) else None)
+    )
+
+    # Try to get chunk from Qdrant first (fast path)
+    if doc_id_int is not None:
+        chunk_text = await _get_chunk_from_qdrant(
+            user_id, doc_id_int, doc_type, chunk_start, chunk_end
+        )
+        if chunk_text:
+            logger.info(
+                f"Retrieved chunk from Qdrant cache for {doc_type} {doc_id} "
+                f"(avoids document re-fetch/re-parse)"
+            )
+
+            # Fetch adjacent chunks for context expansion
+            # Get chunk overlap from config to remove duplicate text
+            from nextcloud_mcp_server.config import get_settings
+
+            settings = get_settings()
+            chunk_overlap = settings.document_chunk_overlap
+
+            before_context = ""
+            after_context = ""
+            has_before_truncation = False
+            has_after_truncation = False
+
+            # Fetch previous chunk if not first chunk
+            if chunk_index > 0:
+                before_chunk = await _get_chunk_by_index_from_qdrant(
+                    user_id, doc_id_int, doc_type, chunk_index - 1
+                )
+                if before_chunk:
+                    # Remove overlap: the last chunk_overlap chars of previous chunk
+                    # overlap with the first chunk_overlap chars of current chunk
+                    before_context = (
+                        before_chunk[:-chunk_overlap]
+                        if len(before_chunk) > chunk_overlap
+                        else ""
+                    )
+                    # Truncate if requested context_chars < remaining length
+                    if before_context and len(before_context) > context_chars:
+                        before_context = before_context[-context_chars:]
+                        has_before_truncation = True
+                else:
+                    # Could not fetch previous chunk, but we're not at start
+                    has_before_truncation = True
+
+            # Fetch next chunk if not last chunk
+            if chunk_index < total_chunks - 1:
+                after_chunk = await _get_chunk_by_index_from_qdrant(
+                    user_id, doc_id_int, doc_type, chunk_index + 1
+                )
+                if after_chunk:
+                    # Remove overlap: the first chunk_overlap chars of next chunk
+                    # overlap with the last chunk_overlap chars of current chunk
+                    after_context = (
+                        after_chunk[chunk_overlap:]
+                        if len(after_chunk) > chunk_overlap
+                        else ""
+                    )
+                    # Truncate if requested context_chars < remaining length
+                    if after_context and len(after_context) > context_chars:
+                        after_context = after_context[:context_chars]
+                        has_after_truncation = True
+                else:
+                    # Could not fetch next chunk, but we're not at end
+                    has_after_truncation = True
+
+            marked_text = _insert_position_markers(
+                before_context=before_context,
+                chunk_text=chunk_text,
+                after_context=after_context,
+                page_number=page_number,
+                chunk_index=chunk_index,
+                total_chunks=total_chunks,
+                has_before_truncation=has_before_truncation,
+                has_after_truncation=has_after_truncation,
+            )
+            return ChunkContext(
+                chunk_text=chunk_text,
+                before_context=before_context,
+                after_context=after_context,
+                chunk_start_offset=chunk_start,
+                chunk_end_offset=chunk_end,
+                page_number=page_number,
+                chunk_index=chunk_index,
+                total_chunks=total_chunks,
+                marked_text=marked_text,
+                has_before_truncation=has_before_truncation,
+                has_after_truncation=has_after_truncation,
+            )
+
+    # Fallback: Fetch full document and extract chunk with context
+    # This path is taken for:
+    # 1. Legacy data with truncated excerpts in Qdrant
+    # 2. Failed Qdrant queries
+    logger.info(
+        f"Falling back to document fetch for {doc_type} {doc_id} "
+        f"(Qdrant cache miss, possibly legacy data)"
+    )
+
+    # For files, retrieve file_path from Qdrant payload
+    resolved_doc_id = doc_id
+    if doc_type == "file" and isinstance(doc_id, int):
+        file_path = await _get_file_path_from_qdrant(
+            user_id, doc_id, chunk_start, chunk_end
+        )
+        if not file_path:
+            logger.warning(
+                f"Could not resolve file_id {doc_id} to file_path from Qdrant"
+            )
+            return None
+        resolved_doc_id = file_path
+        logger.debug(f"Resolved file_id {doc_id} to file_path {file_path}")
+
+    # Fetch full document text
+    full_text = await _fetch_document_text(nc_client, resolved_doc_id, doc_type)
+    if full_text is None:
+        logger.warning(
+            f"Could not fetch document text for {doc_type} {doc_id}, "
+            "skipping context expansion"
+        )
+        return None
+
+    # Validate offsets
+    if chunk_start < 0 or chunk_end > len(full_text) or chunk_start >= chunk_end:
+        logger.warning(
+            f"Invalid chunk offsets for {doc_type} {doc_id}: "
+            f"start={chunk_start}, end={chunk_end}, doc_len={len(full_text)}"
+        )
+        return None
+
+    # Extract chunk text
+    chunk_text = full_text[chunk_start:chunk_end]
+
+    # Calculate context boundaries
+    context_start = max(0, chunk_start - context_chars)
+    context_end = min(len(full_text), chunk_end + context_chars)
+
+    # Extract context
+    before_context = full_text[context_start:chunk_start]
+    after_context = full_text[chunk_end:context_end]
+
+    # Check for truncation
+    has_before_truncation = context_start > 0
+    has_after_truncation = context_end < len(full_text)
+
+    # Create marked text with position markers
+    marked_text = _insert_position_markers(
+        before_context=before_context,
+        chunk_text=chunk_text,
+        after_context=after_context,
+        page_number=page_number,
+        chunk_index=chunk_index,
+        total_chunks=total_chunks,
+        has_before_truncation=has_before_truncation,
+        has_after_truncation=has_after_truncation,
+    )
+
+    return ChunkContext(
+        chunk_text=chunk_text,
+        before_context=before_context,
+        after_context=after_context,
+        chunk_start_offset=chunk_start,
+        chunk_end_offset=chunk_end,
+        page_number=page_number,
+        chunk_index=chunk_index,
+        total_chunks=total_chunks,
+        marked_text=marked_text,
+        has_before_truncation=has_before_truncation,
+        has_after_truncation=has_after_truncation,
+    )
+
+
+async def _fetch_document_text(
+    nc_client: NextcloudClient, doc_id: str | int, doc_type: str
+) -> str | None:
+    """Fetch full text content of a document.
+
+    Args:
+        nc_client: Authenticated Nextcloud client
+        doc_id: Document ID (note ID or file path)
+        doc_type: Type of document ("note", "file", etc.)
+
+    Returns:
+        Full document text, or None if document cannot be retrieved
+    """
+    try:
+        if doc_type == "note":
+            # Fetch note by ID
+            note = await nc_client.notes.get_note(note_id=int(doc_id))
+            # Reconstruct full content as indexed: title + "\n\n" + content
+            # This ensures chunk offsets align with indexed content structure
+            title = note.get("title", "")
+            content = note.get("content", "")
+            return f"{title}\n\n{content}"
+        elif doc_type == "file":
+            # Fetch file content via WebDAV
+            try:
+                file_path = str(doc_id)
+                file_content, content_type = await nc_client.webdav.read_file(file_path)
+
+                # Check if it's a PDF (by content type or file extension)
+                is_pdf = (
+                    content_type and "pdf" in content_type.lower()
+                ) or file_path.lower().endswith(".pdf")
+
+                if is_pdf:
+                    # Extract text from PDF using PyMuPDF
+                    # IMPORTANT: Use pymupdf4llm.to_markdown() to match indexing extraction
+                    # This ensures character offsets align between indexed chunks and retrieval
+                    import pymupdf
+                    import pymupdf4llm
+
+                    logger.debug(f"Extracting text from PDF: {file_path}")
+                    pdf_doc = pymupdf.open(stream=file_content, filetype="pdf")
+                    text_parts = []
+
+                    # Extract each page as markdown (same as indexing)
+                    for page_num in range(pdf_doc.page_count):
+                        page_md = pymupdf4llm.to_markdown(
+                            pdf_doc,
+                            pages=[page_num],
+                            write_images=False,  # Don't need images for context
+                            page_chunks=False,
+                        )
+                        text_parts.append(page_md)
+
+                    pdf_doc.close()
+
+                    # Join pages (no separator - matches indexing)
+                    full_text = "".join(text_parts)
+                    logger.debug(
+                        f"Extracted {len(full_text)} characters from "
+                        f"{pdf_doc.page_count} pages in {file_path}"
+                    )
+                    return full_text
+                else:
+                    # Assume it's a text file, decode to string
+                    logger.debug(f"Decoding text file: {file_path}")
+                    return file_content.decode("utf-8", errors="replace")
+            except Exception as e:
+                logger.error(
+                    f"Error fetching file content for {doc_id}: {e}", exc_info=True
+                )
+                return None
+        else:
+            logger.warning(f"Unsupported doc_type for context expansion: {doc_type}")
+            return None
+    except Exception as e:
+        logger.error(f"Error fetching document {doc_type} {doc_id}: {e}", exc_info=True)
+        return None
+
+
+def _insert_position_markers(
+    before_context: str,
+    chunk_text: str,
+    after_context: str,
+    page_number: int | None,
+    chunk_index: int,
+    total_chunks: int,
+    has_before_truncation: bool,
+    has_after_truncation: bool,
+) -> str:
+    """Insert position markers around matched chunk.
+
+    Creates markdown-formatted text with visual markers indicating chunk
+    boundaries and metadata.
+
+    Args:
+        before_context: Text before chunk
+        chunk_text: The matched chunk
+        after_context: Text after chunk
+        page_number: Optional page number
+        chunk_index: Zero-based chunk index
+        total_chunks: Total chunks in document
+        has_before_truncation: Whether before_context is truncated
+        has_after_truncation: Whether after_context is truncated
+
+    Returns:
+        Formatted text with position markers
+    """
+    # Build position metadata
+    position_parts = []
+    if page_number is not None:
+        position_parts.append(f"Page {page_number}")
+    position_parts.append(f"Chunk {chunk_index + 1} of {total_chunks}")
+    position_metadata = ", ".join(position_parts)
+
+    # Build marked text
+    parts = []
+
+    # Add truncation indicator for before context
+    if has_before_truncation:
+        parts.append("**[...]**\n\n")
+
+    # Add before context if present
+    if before_context:
+        parts.append(before_context)
+
+    # Add chunk start marker
+    parts.append(f"\n\n🔍 **MATCHED CHUNK START** ({position_metadata})\n\n")
+
+    # Add chunk text
+    parts.append(chunk_text)
+
+    # Add chunk end marker
+    parts.append("\n\n🔍 **MATCHED CHUNK END**\n\n")
+
+    # Add after context if present
+    if after_context:
+        parts.append(after_context)
+
+    # Add truncation indicator for after context
+    if has_after_truncation:
+        parts.append("\n\n**[...]**")
+
+    return "".join(parts)

nextcloud_mcp_server/search/pdf_highlighter.py

@@ -0,0 +1,907 @@
+"""PDF chunk highlighting utilities for vector visualization.
+
+This module provides utilities to generate highlighted page images showing
+matched chunks and their context from semantic search results.
+
+The highlighting uses character offsets to precisely locate chunks within
+PDF documents, ensuring accurate highlighting even when text formatting
+varies between indexing and rendering.
+"""
+
+import logging
+import re
+from typing import Optional
+
+import pymupdf
+import pymupdf4llm
+
+logger = logging.getLogger(__name__)
+
+
+class PDFHighlighter:
+    """Generate highlighted page images from PDF chunks."""
+
+    # Color definitions (RGB, 0-1 range)
+    COLORS = {
+        "yellow": [1, 1, 0],
+        "red": [1, 0, 0],
+        "green": [0, 1, 0],
+        "blue": [0, 0, 1],
+        "orange": [1, 0.5, 0],
+        "pink": [1, 0, 1],
+        "gray": [0.7, 0.7, 0.7],
+        "light_blue": [0.7, 0.9, 1.0],
+        "light_green": [0.7, 1.0, 0.7],
+    }
+
+    @staticmethod
+    def strip_markdown(text: str) -> str:
+        """Remove markdown formatting to improve search accuracy.
+
+        Args:
+            text: Text with potential markdown formatting
+
+        Returns:
+            Plain text with markdown removed
+        """
+        # Remove bold/italic markers
+        text = re.sub(r"\*\*(.+?)\*\*", r"\1", text)
+        text = re.sub(r"\*(.+?)\*", r"\1", text)
+        text = re.sub(r"__(.+?)__", r"\1", text)
+        text = re.sub(r"_(.+?)_", r"\1", text)
+
+        # Remove headers
+        text = re.sub(r"^#+\s+", "", text, flags=re.MULTILINE)
+
+        # Remove inline code
+        text = re.sub(r"`(.+?)`", r"\1", text)
+
+        return text.strip()
+
+    @staticmethod
+    def extract_pdf_text_with_boundaries(
+        pdf_doc: pymupdf.Document,
+    ) -> tuple[str, list[dict]]:
+        """Extract full document text with page boundary tracking.
+
+        Uses pymupdf4llm.to_markdown() for consistency with indexing.
+
+        IMPORTANT: Must use write_images=True to match PyMuPDFProcessor behavior!
+        Even though we don't need the images, we need the image references in the
+        markdown text to maintain consistent character offsets with indexing.
+
+        Args:
+            pdf_doc: Open PyMuPDF document
+
+        Returns:
+            Tuple of (full_text, page_boundaries) where page_boundaries is a list of:
+            {"page": 1, "start_offset": 0, "end_offset": 1234}
+        """
+        import tempfile
+        from pathlib import Path
+
+        page_boundaries = []
+        text_parts = []
+        current_offset = 0
+
+        # Use temp directory for image output (images are discarded after extraction)
+        temp_dir = Path(tempfile.mkdtemp(prefix="pdf_highlight_"))
+
+        for page_idx in range(pdf_doc.page_count):
+            page_md = pymupdf4llm.to_markdown(
+                pdf_doc,
+                pages=[page_idx],
+                write_images=True,  # Must match indexing! Otherwise offsets misalign
+                image_path=temp_dir,
+                page_chunks=False,
+            )
+
+            page_boundaries.append(
+                {
+                    "page": page_idx + 1,  # 1-indexed
+                    "start_offset": current_offset,
+                    "end_offset": current_offset + len(page_md),
+                }
+            )
+
+            text_parts.append(page_md)
+            current_offset += len(page_md)
+
+        full_text = "".join(text_parts)
+
+        # Clean up temp directory and extracted images
+        import shutil
+
+        try:
+            shutil.rmtree(temp_dir)
+        except Exception as e:
+            logger.warning(f"Failed to clean up temp directory {temp_dir}: {e}")
+
+        return full_text, page_boundaries
+
+    @staticmethod
+    def find_chunk_page(
+        chunk_start_offset: int,
+        chunk_end_offset: int,
+        page_boundaries: list[dict],
+    ) -> Optional[dict]:
+        """Find which page contains the most of a given chunk.
+
+        Args:
+            chunk_start_offset: Chunk start position in full document
+            chunk_end_offset: Chunk end position in full document
+            page_boundaries: Page boundary list from extract_pdf_text_with_boundaries()
+
+        Returns:
+            Dict with keys: page_num, overlap_chars, page_relative_start, page_relative_end
+            or None if chunk not found on any page
+        """
+        chunk_pages = []
+
+        for boundary in page_boundaries:
+            page_start = boundary["start_offset"]
+            page_end = boundary["end_offset"]
+
+            # Check if chunk overlaps with this page
+            if chunk_start_offset < page_end and chunk_end_offset > page_start:
+                overlap_start = max(chunk_start_offset, page_start)
+                overlap_end = min(chunk_end_offset, page_end)
+                overlap_chars = overlap_end - overlap_start
+
+                chunk_pages.append(
+                    {
+                        "page_num": boundary["page"],
+                        "overlap_chars": overlap_chars,
+                        "page_relative_start": overlap_start - page_start,
+                        "page_relative_end": overlap_end - page_start,
+                    }
+                )
+
+        if not chunk_pages:
+            return None
+
+        # Return page with maximum overlap
+        return max(chunk_pages, key=lambda p: p["overlap_chars"])
+
+    @staticmethod
+    def highlight_chunk_by_word_positions(
+        page: pymupdf.Page,
+        chunk_text: str,
+        color: str = "yellow",
+        search_region: tuple[float, float, float, float] | None = None,
+    ) -> int:
+        """Highlight chunk using word-position matching.
+
+        This method matches words from the chunk to their positions on the PDF page,
+        avoiding text search mismatches between markdown-formatted text and raw PDF text.
+
+        Args:
+            page: PyMuPDF page object
+            chunk_text: Text to highlight (may contain markdown)
+            color: Color name from COLORS dict
+            search_region: Optional (x0, y0, x1, y1) bounding box to constrain search.
+                          If provided, only words within this region are considered.
+
+        Returns:
+            Number of highlight rectangles added
+        """
+        # Tokenize chunk into words (alphanumeric only, lowercase)
+        chunk_words = re.findall(
+            r"\w+", PDFHighlighter.strip_markdown(chunk_text).lower()
+        )
+
+        if not chunk_words:
+            logger.warning("No words found in chunk text")
+            return 0
+
+        # Get all words from page with positions
+        # Format: (x0, y0, x1, y1, "word", block_no, line_no, word_no)
+        try:
+            page_words = page.get_text("words")
+        except Exception as e:
+            logger.error(f"Failed to extract words from page: {e}")
+            return 0
+
+        if not page_words:
+            logger.warning("No words found on page")
+            return 0
+
+        # Filter words by search region if provided
+        if search_region:
+            rx0, ry0, rx1, ry1 = search_region
+            # Allow some tolerance (10 points) for words near region boundary
+            tolerance = 10
+            page_words = [
+                w
+                for w in page_words
+                if (
+                    w[0] >= rx0 - tolerance
+                    and w[2] <= rx1 + tolerance
+                    and w[1] >= ry0 - tolerance
+                    and w[3] <= ry1 + tolerance
+                )
+            ]
+            logger.debug(
+                f"Filtered to {len(page_words)} words in region "
+                f"({rx0:.0f}, {ry0:.0f}, {rx1:.0f}, {ry1:.0f})"
+            )
+
+        if not page_words:
+            logger.warning("No words found in search region")
+            return 0
+
+        # Find matching word sequence - use FIRST match, not longest
+        # This ensures we highlight the actual chunk location, not similar text elsewhere
+        matches = []
+
+        # Build a simple word-to-positions index for the first few chunk words
+        # to find candidate starting positions
+        first_chunk_word = chunk_words[0] if chunk_words else ""
+        candidate_starts = []
+
+        for i, pw in enumerate(page_words):
+            page_word = pw[4].lower()
+            # Check if this could be the start of the chunk
+            if (
+                first_chunk_word == page_word
+                or first_chunk_word in page_word
+                or page_word in first_chunk_word
+            ):
+                candidate_starts.append(i)
+
+        # Try each candidate start position and take the FIRST good match
+        for start_pos in candidate_starts:
+            current_matches = []
+            chunk_idx = 0
+            skip_count = 0
+            max_skips = 3  # Allow some formatting differences
+
+            for page_idx in range(start_pos, len(page_words)):
+                if chunk_idx >= len(chunk_words):
+                    break
+
+                page_word = page_words[page_idx][4].lower()
+                chunk_word = chunk_words[chunk_idx]
+
+                # Check for match (allow partial matches for flexibility)
+                if (
+                    chunk_word == page_word
+                    or chunk_word in page_word
+                    or page_word in chunk_word
+                ):
+                    current_matches.append(page_words[page_idx])
+                    chunk_idx += 1
+                    skip_count = 0
+                elif skip_count < max_skips:
+                    # Allow skipping some words (formatting, punctuation)
+                    skip_count += 1
+                    continue
+                else:
+                    break
+
+            # Accept if we matched at least 50% of chunk words
+            if len(current_matches) >= len(chunk_words) * 0.5:
+                matches = current_matches
+                logger.debug(
+                    f"Found match at position {start_pos}: "
+                    f"{len(matches)}/{len(chunk_words)} words"
+                )
+                break  # Take FIRST match, not best/longest
+
+        if not matches:
+            logger.debug(f"No word matches found (chunk has {len(chunk_words)} words)")
+            return 0
+
+        logger.debug(
+            f"Matched {len(matches)} words out of {len(chunk_words)} chunk words"
+        )
+
+        # Build rectangles from matched words
+        rects = [pymupdf.Rect(w[0], w[1], w[2], w[3]) for w in matches]
+
+        # Check if matches are contiguous (not scattered across the page)
+        # Scattered matches indicate false positives from common words
+        if len(rects) > 1:
+            # Sort by vertical position then horizontal
+            sorted_matches = sorted(matches, key=lambda w: (round(w[1]), w[0]))
+
+            # Check for large vertical gaps (more than ~2 lines apart)
+            # A typical line height is 12-20 points
+            max_line_gap = 50  # Points - allows for ~2-3 lines gap
+            prev_y = sorted_matches[0][1]
+            large_gaps = 0
+
+            for match in sorted_matches[1:]:
+                y_gap = match[1] - prev_y
+                if y_gap > max_line_gap:
+                    large_gaps += 1
+                prev_y = match[1]
+
+            # If matches are scattered (many large gaps), reject this match
+            # A chunk should be mostly contiguous text
+            if large_gaps > len(matches) * 0.3:  # More than 30% have gaps
+                logger.debug(
+                    f"Rejecting scattered matches: {large_gaps} large gaps "
+                    f"out of {len(matches)} matches"
+                )
+                return 0
+
+        # Merge adjacent rectangles on the same line for cleaner highlighting
+        merged_rects = []
+        sorted_rects = sorted(rects, key=lambda r: (round(r.y0), r.x0))
+
+        current_rect = None
+        for rect in sorted_rects:
+            if current_rect is None:
+                current_rect = rect
+            elif abs(rect.y0 - current_rect.y0) < 5:  # Same line (within 5 points)
+                current_rect = current_rect | rect  # Union
+            else:
+                merged_rects.append(current_rect)
+                current_rect = rect
+
+        if current_rect:
+            merged_rects.append(current_rect)
+
+        # Add highlights
+        rgb = PDFHighlighter.COLORS.get(color, PDFHighlighter.COLORS["yellow"])
+        for rect in merged_rects:
+            highlight = page.add_highlight_annot(rect)
+            highlight.set_colors({"stroke": rgb})
+            highlight.set_info(
+                content="Chunk from semantic search",
+                title="PDF Highlighter (word-position)",
+            )
+            highlight.update()
+
+        return len(merged_rects)
+
+    @staticmethod
+    def find_unique_phrase(
+        text: str, min_len: int = 30, max_len: int = 80
+    ) -> str | None:
+        """Find a relatively unique phrase from text for location search.
+
+        Looks for phrases that are likely to be unique on the page:
+        - Prefers phrases with numbers or special terms
+        - Avoids very common words
+
+        Args:
+            text: Source text to extract phrase from
+            min_len: Minimum phrase length
+            max_len: Maximum phrase length
+
+        Returns:
+            A phrase likely to be unique, or None if not found
+        """
+        clean_text = PDFHighlighter.strip_markdown(text).strip()
+        if not clean_text:
+            return None
+
+        # Try first sentence (often unique due to context)
+        sentences = re.split(r"[.!?]\s+", clean_text)
+        for sentence in sentences:
+            sentence = sentence.strip()
+            if min_len <= len(sentence) <= max_len:
+                return sentence
+            elif len(sentence) > max_len:
+                return sentence[:max_len]
+
+        # Fallback: first N chars
+        if len(clean_text) >= min_len:
+            return clean_text[:max_len]
+
+        return clean_text if clean_text else None
+
+    @staticmethod
+    def _find_chunk_bbox(
+        page: pymupdf.Page,
+        chunk_text: str,
+        page_relative_start: int,
+        page_relative_end: int,
+        page_text_length: int,
+    ) -> tuple[float, float, float, float] | None:
+        """Find bounding box for a chunk without modifying the page.
+
+        Returns (x0, y0, x1, y1) in page coordinates, or None if not found.
+        """
+        page_rect = page.rect
+
+        # Strip markdown for searching
+        search_text = PDFHighlighter.strip_markdown(chunk_text)
+
+        # Try to find chunk location using text search
+        anchor_rect = None
+        search_phrases = []
+
+        # Build search phrases from chunk text
+        sentences = re.split(r"[.!?]\s+", search_text)
+        for sentence in sentences[:3]:
+            sentence = sentence.strip()
+            if len(sentence) >= 20:
+                search_phrases.append(sentence[:80])
+                if len(sentence) >= 40:
+                    search_phrases.append(sentence[:40])
+
+        # Also try first N characters
+        if len(search_text) >= 30:
+            search_phrases.append(search_text[:60])
+            search_phrases.append(search_text[:30])
+
+        for phrase in search_phrases:
+            if not phrase:
+                continue
+            rects = page.search_for(phrase.strip())
+            if rects:
+                anchor_rect = rects[0]
+                break
+
+        if not anchor_rect:
+            return None
+
+        # Calculate chunk height based on character count
+        chunk_chars = len(search_text)
+        estimated_lines = max(1, chunk_chars / 60)
+        estimated_height = estimated_lines * 14
+
+        # Build bounding box
+        return (
+            page_rect.x0 + 30,  # Left margin
+            anchor_rect.y0 - 5,  # Start slightly above anchor
+            page_rect.x1 - 30,  # Right margin
+            min(anchor_rect.y0 + estimated_height + 10, page_rect.y1 - 30),
+        )
+
+    @staticmethod
+    def highlight_chunk_on_page(
+        page: pymupdf.Page,
+        chunk_text: str,
+        color: str = "yellow",
+        page_relative_start: int | None = None,
+        page_relative_end: int | None = None,
+        page_text_length: int | None = None,
+    ) -> int:
+        """Add bounding box highlight to a PDF page for the given chunk text.
+
+        Uses text search to find the chunk's location on the page, then draws
+        a bounding box around that region. Falls back to character offset estimation
+        if text search fails.
+
+        Args:
+            page: PyMuPDF page object
+            chunk_text: Text to highlight (may contain markdown)
+            color: Color name from COLORS dict
+            page_relative_start: Character offset where chunk starts on page (optional)
+            page_relative_end: Character offset where chunk ends on page (optional)
+            page_text_length: Total character length of page text (optional)
+
+        Returns:
+            Number of highlights added (1 for bounding box, 0 if failed)
+        """
+        page_rect = page.rect
+        rgb = PDFHighlighter.COLORS.get(color, PDFHighlighter.COLORS["yellow"])
+
+        # Strip markdown for searching
+        search_text = PDFHighlighter.strip_markdown(chunk_text)
+
+        # Try to find chunk location using text search
+        # Search for progressively shorter phrases until we find a match
+        anchor_rect = None
+        search_phrases = []
+
+        # Build search phrases from chunk text
+        sentences = re.split(r"[.!?]\s+", search_text)
+        for sentence in sentences[:3]:  # Try first 3 sentences
+            sentence = sentence.strip()
+            if len(sentence) >= 20:
+                search_phrases.append(sentence[:80])
+                if len(sentence) >= 40:
+                    search_phrases.append(sentence[:40])
+
+        # Also try first N characters
+        if len(search_text) >= 30:
+            search_phrases.append(search_text[:60])
+            search_phrases.append(search_text[:30])
+
+        for phrase in search_phrases:
+            if not phrase:
+                continue
+            rects = page.search_for(phrase.strip())
+            if rects:
+                anchor_rect = rects[0]  # Use first match
+                logger.debug(f"Found chunk anchor using phrase: '{phrase[:30]}...'")
+                break
+
+        if not anchor_rect:
+            page_num = page.number + 1 if page.number is not None else "unknown"
+            logger.warning(f"Could not find chunk text on page {page_num}")
+            return 0
+
+        # Calculate chunk height based on character count
+        # Estimate ~15 chars per line, ~12pt line height
+        chunk_chars = len(search_text)
+        estimated_lines = max(1, chunk_chars / 60)  # ~60 chars per line typical
+        estimated_height = estimated_lines * 14  # ~14pt per line
+
+        # Build bounding box starting from anchor
+        chunk_rect = pymupdf.Rect(
+            page_rect.x0 + 30,  # Left margin
+            anchor_rect.y0 - 5,  # Start slightly above anchor
+            page_rect.x1 - 30,  # Right margin
+            min(
+                anchor_rect.y0 + estimated_height + 10, page_rect.y1 - 30
+            ),  # Estimated bottom
+        )
+
+        # Draw a visible rectangle around the chunk region
+        shape = page.new_shape()
+        shape.draw_rect(chunk_rect)
+        shape.finish(
+            color=rgb,  # Border color
+            fill=None,  # No fill (transparent)
+            width=2.5,  # Border width
+            dashes="[4 2]",  # Dashed line
+        )
+        shape.commit()
+
+        # Add semi-transparent fill for visibility
+        fill_shape = page.new_shape()
+        fill_shape.draw_rect(chunk_rect)
+        fill_shape.finish(
+            color=None,  # No border
+            fill=[1, 1, 0.7],  # Light yellow fill
+            fill_opacity=0.15,  # Very transparent
+        )
+        fill_shape.commit()
+
+        logger.debug(
+            f"Added bounding box at y={chunk_rect.y0:.0f}-{chunk_rect.y1:.0f} "
+            f"(estimated {estimated_lines:.1f} lines)"
+        )
+
+        return 1
+
+    @staticmethod
+    def highlight_chunk(
+        pdf_bytes: bytes,
+        chunk_start_offset: int,
+        chunk_end_offset: int,
+        stored_page_number: Optional[int] = None,
+        color: str = "yellow",
+        zoom: float = 2.0,
+    ) -> Optional[tuple[bytes, int, int]]:
+        """Generate PNG image of PDF page with highlighted chunk.
+
+        This is the main entry point for highlighting. It:
+        1. Extracts document text with page boundaries
+        2. Finds which page contains the chunk
+        3. Extracts chunk text using character offsets
+        4. Highlights the chunk on the page
+        5. Renders page to PNG
+
+        Args:
+            pdf_bytes: PDF file bytes
+            chunk_start_offset: Chunk start position (document-level)
+            chunk_end_offset: Chunk end position (document-level)
+            stored_page_number: Page number from metadata (optional, for validation)
+            color: Highlight color name
+            zoom: Rendering zoom factor (2.0 = 144 DPI)
+
+        Returns:
+            Tuple of (png_bytes, page_number, highlight_count) or None if failed
+        """
+        import tempfile
+        from pathlib import Path
+
+        temp_pdf_path = None
+        try:
+            # Write PDF to temp file with consistent name "pdf.pdf"
+            # This ensures image references match indexing (e.g., pdf-0001.png)
+            # Different temp filenames would cause different markdown text lengths!
+            temp_dir = Path(tempfile.mkdtemp(prefix="pdf_highlight_"))
+            temp_pdf_path = temp_dir / "pdf.pdf"
+            temp_pdf_path.write_bytes(pdf_bytes)
+
+            # Open PDF from temp file
+            doc = pymupdf.open(temp_pdf_path)
+
+            # Extract text with page boundaries
+            full_text, page_boundaries = (
+                PDFHighlighter.extract_pdf_text_with_boundaries(doc)
+            )
+
+            # Find which page contains the chunk
+            chunk_page_info = PDFHighlighter.find_chunk_page(
+                chunk_start_offset, chunk_end_offset, page_boundaries
+            )
+
+            if not chunk_page_info:
+                logger.error("Chunk not found on any page")
+                doc.close()
+                return None
+
+            page_num = chunk_page_info["page_num"]
+
+            # Log if page differs from stored metadata
+            if stored_page_number and stored_page_number != page_num:
+                logger.info(
+                    f"Chunk primarily on page {page_num}, metadata says {stored_page_number}"
+                )
+
+            # Extract page text
+            page_boundary = page_boundaries[page_num - 1]
+            page_start = page_boundary["start_offset"]
+            page_end = page_boundary["end_offset"]
+            page_text = full_text[page_start:page_end]
+
+            # Extract chunk text using page-relative offsets
+            page_relative_start = chunk_page_info["page_relative_start"]
+            page_relative_end = chunk_page_info["page_relative_end"]
+            chunk_text = page_text[page_relative_start:page_relative_end]
+
+            # Calculate page text length for region estimation
+            page_text_length = page_end - page_start
+
+            logger.debug(
+                f"Extracted {len(chunk_text)} chars on page {page_num} "
+                f"(offsets {page_relative_start}-{page_relative_end} of {page_text_length})"
+            )
+
+            # Get page and add highlights
+            page = doc[page_num - 1]
+            highlight_count = PDFHighlighter.highlight_chunk_on_page(
+                page,
+                chunk_text,
+                color,
+                page_relative_start=page_relative_start,
+                page_relative_end=page_relative_end,
+                page_text_length=page_text_length,
+            )
+
+            if highlight_count == 0:
+                logger.warning("No highlights added")
+                doc.close()
+                return None
+
+            # Render page to PNG
+            mat = pymupdf.Matrix(zoom, zoom)
+            pix = page.get_pixmap(matrix=mat, alpha=False)
+            png_bytes = pix.tobytes("png")
+
+            doc.close()
+
+            logger.info(
+                f"Generated {len(png_bytes):,} byte image with {highlight_count} highlights"
+            )
+
+            return (png_bytes, page_num, highlight_count)
+
+        except Exception as e:
+            logger.error(f"Error highlighting chunk: {e}", exc_info=True)
+            return None
+
+        finally:
+            # Clean up temp directory and PDF file
+            if temp_pdf_path and temp_pdf_path.parent.exists():
+                try:
+                    import shutil
+
+                    shutil.rmtree(temp_pdf_path.parent)
+                except Exception as e:
+                    logger.warning(
+                        f"Failed to delete temp directory {temp_pdf_path.parent}: {e}"
+                    )
+
+    @staticmethod
+    def highlight_chunks_batch(
+        pdf_bytes: bytes,
+        chunks: list[tuple[int, int, int, int | None, str]],
+        page_boundaries: list[dict],
+        full_text: str,
+        color: str = "yellow",
+        zoom: float = 2.0,
+    ) -> dict[int, tuple[bytes, int, int]]:
+        """Generate highlighted images for multiple chunks.
+
+        Opens PDF once for rendering, uses pre-computed page boundaries from the
+        document processor. This ensures consistent character offsets between
+        chunking and highlighting.
+
+        Args:
+            pdf_bytes: PDF file bytes
+            chunks: List of (chunk_index, start_offset, end_offset, stored_page_number, chunk_text)
+                    The chunk_index is used as the key in the returned dict.
+                    chunk_text is the actual text content of the chunk.
+            page_boundaries: Pre-computed page boundaries from document processor.
+                            Each entry: {"page": 1, "start_offset": 0, "end_offset": 1234}
+            full_text: Full document text for extracting page-relative portions.
+            color: Highlight color name
+            zoom: Rendering zoom factor (2.0 = 144 DPI)
+
+        Returns:
+            Dict mapping chunk_index to (png_bytes, page_number, highlight_count)
+            Chunks that fail to highlight are omitted from the result.
+        """
+        import shutil
+        import tempfile
+        from collections import defaultdict
+        from pathlib import Path
+
+        results: dict[int, tuple[bytes, int, int]] = {}
+
+        if not chunks:
+            return results
+
+        temp_pdf_path = None
+        try:
+            # Write PDF to temp file
+            temp_dir = Path(tempfile.mkdtemp(prefix="pdf_highlight_batch_"))
+            temp_pdf_path = temp_dir / "pdf.pdf"
+            temp_pdf_path.write_bytes(pdf_bytes)
+
+            # Open PDF once (only for rendering, not text extraction)
+            doc = pymupdf.open(temp_pdf_path)
+
+            logger.debug(
+                f"Batch highlighting: {len(chunks)} chunks, "
+                f"{len(page_boundaries)} pages"
+            )
+
+            # Group chunks by their target page for efficient rendering
+            # We'll render each page only once with all its highlights
+            chunks_by_page: dict[int, list[tuple[int, dict, str]]] = defaultdict(list)
+
+            for chunk_tuple in chunks:
+                # Unpack chunk tuple - chunk_text is now passed directly
+                chunk_index, start_offset, end_offset, stored_page_num, chunk_text = (
+                    chunk_tuple
+                )
+
+                # Find which page contains this chunk
+                chunk_page_info = PDFHighlighter.find_chunk_page(
+                    start_offset, end_offset, page_boundaries
+                )
+
+                if not chunk_page_info:
+                    logger.warning(f"Chunk {chunk_index}: not found on any page")
+                    continue
+
+                page_num = chunk_page_info["page_num"]
+
+                # Log if page differs from stored metadata
+                if stored_page_num and stored_page_num != page_num:
+                    logger.debug(
+                        f"Chunk {chunk_index}: found on page {page_num}, "
+                        f"metadata says {stored_page_num}"
+                    )
+
+                # Extract page-relative portion of chunk text
+                # This is critical for cross-page chunks where the start
+                # of the chunk might be on a different page
+                page_boundary = page_boundaries[page_num - 1]
+                page_start = page_boundary["start_offset"]
+                page_end = page_boundary["end_offset"]
+                page_text_length = page_end - page_start
+
+                # Calculate what portion of the chunk appears on this page
+                chunk_start_on_page = max(start_offset, page_start)
+                chunk_end_on_page = min(end_offset, page_end)
+
+                # Extract just the text that appears on this page
+                page_relative_text = full_text[chunk_start_on_page:chunk_end_on_page]
+
+                chunks_by_page[page_num].append(
+                    (chunk_index, chunk_page_info, page_relative_text, page_text_length)
+                )
+
+            logger.debug(
+                f"Chunks distributed across {len(chunks_by_page)} unique pages"
+            )
+
+            # OPTIMIZATION: Render each page ONCE, then draw highlights using PIL
+            # This avoids expensive page.get_pixmap() calls per chunk
+            from io import BytesIO
+
+            from PIL import Image, ImageDraw
+
+            # PIL color for bounding box (RGB tuple)
+            rgb = PDFHighlighter.COLORS.get(color, PDFHighlighter.COLORS["yellow"])
+            pil_color = tuple(int(c * 255) for c in rgb)
+            fill_color = (255, 255, 178, 38)  # Light yellow with alpha
+
+            for page_num, page_chunks in chunks_by_page.items():
+                page = doc[page_num - 1]
+
+                # Render page ONCE to get base image (most expensive operation)
+                mat = pymupdf.Matrix(zoom, zoom)
+                base_pix = page.get_pixmap(matrix=mat, alpha=False)
+                base_png = base_pix.tobytes("png")
+
+                # Convert to PIL Image for fast highlight drawing
+                base_image = Image.open(BytesIO(base_png)).convert("RGBA")
+                page_rect = page.rect
+
+                logger.debug(
+                    f"Page {page_num}: rendered once, processing {len(page_chunks)} chunks"
+                )
+
+                for (
+                    chunk_index,
+                    chunk_page_info,
+                    chunk_text,
+                    page_text_length,
+                ) in page_chunks:
+                    try:
+                        # Find chunk bounding box using text search
+                        bbox = PDFHighlighter._find_chunk_bbox(
+                            page,
+                            chunk_text,
+                            chunk_page_info["page_relative_start"],
+                            chunk_page_info["page_relative_end"],
+                            page_text_length,
+                        )
+
+                        if bbox is None:
+                            logger.warning(f"Chunk {chunk_index}: could not find bbox")
+                            continue
+
+                        # Copy base image for this chunk
+                        chunk_image = base_image.copy()
+
+                        # Scale bbox coordinates to pixmap coordinates
+                        scale_x = base_pix.width / page_rect.width
+                        scale_y = base_pix.height / page_rect.height
+                        pil_bbox = (
+                            int(bbox[0] * scale_x),
+                            int(bbox[1] * scale_y),
+                            int(bbox[2] * scale_x),
+                            int(bbox[3] * scale_y),
+                        )
+
+                        # Create transparent overlay for fill (proper alpha blending)
+                        overlay = Image.new("RGBA", chunk_image.size, (0, 0, 0, 0))
+                        overlay_draw = ImageDraw.Draw(overlay)
+                        overlay_draw.rectangle(pil_bbox, fill=fill_color)
+
+                        # Alpha composite the overlay onto the chunk image
+                        chunk_image = Image.alpha_composite(chunk_image, overlay)
+
+                        # Draw border on top (solid, not transparent)
+                        border_draw = ImageDraw.Draw(chunk_image)
+                        border_draw.rectangle(pil_bbox, outline=pil_color, width=3)
+
+                        # Convert back to PNG bytes
+                        output = BytesIO()
+                        chunk_image.convert("RGB").save(output, format="PNG")
+                        png_bytes = output.getvalue()
+
+                        results[chunk_index] = (png_bytes, page_num, 1)
+
+                        logger.debug(
+                            f"Chunk {chunk_index}: {len(png_bytes):,} bytes, "
+                            f"page {page_num}, bbox {pil_bbox}"
+                        )
+
+                    except Exception as e:
+                        logger.error(f"Chunk {chunk_index}: error - {e}")
+                        continue
+
+            doc.close()
+
+            logger.info(
+                f"Batch highlighted {len(results)}/{len(chunks)} chunks successfully"
+            )
+
+            return results
+
+        except Exception as e:
+            logger.error(f"Error in batch highlighting: {e}", exc_info=True)
+            return results
+
+        finally:
+            # Clean up temp directory
+            if temp_pdf_path and temp_pdf_path.parent.exists():
+                try:
+                    shutil.rmtree(temp_pdf_path.parent)
+                except Exception as e:
+                    logger.warning(f"Failed to clean up temp dir: {e}")

nextcloud_mcp_server/search/semantic.py

@@ -9,6 +9,7 @@ from nextcloud_mcp_server.config import get_settings
 from nextcloud_mcp_server.embedding import get_embedding_service
 from nextcloud_mcp_server.observability.metrics import record_qdrant_operation
 from nextcloud_mcp_server.search.algorithms import SearchAlgorithm, SearchResult
+from nextcloud_mcp_server.vector.placeholder import get_placeholder_filter
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
 logger = logging.getLogger(__name__)
@@ -50,6 +51,9 @@ class SemanticSearchAlgorithm(SearchAlgorithm):
         Returns unverified results from Qdrant. Access verification should be
         performed separately at the final output stage using verify_search_results().
 
+        Deduplicates by (doc_id, doc_type, chunk_start_offset, chunk_end_offset)
+        to show multiple chunks from the same document while avoiding duplicate chunks.
+
         Args:
             query: Natural language search query
             user_id: User ID for filtering
@@ -74,16 +78,19 @@ class SemanticSearchAlgorithm(SearchAlgorithm):
         # Generate embedding for query
         embedding_service = get_embedding_service()
         query_embedding = await embedding_service.embed(query)
+        # Store for reuse by callers (e.g., viz_routes PCA visualization)
+        self.query_embedding = query_embedding
         logger.debug(
             f"Generated embedding for query (dimension={len(query_embedding)})"
         )
 
         # Build Qdrant filter
         filter_conditions = [
+            get_placeholder_filter(),  # Always exclude placeholders from user-facing queries
             FieldCondition(
                 key="user_id",
                 match=MatchValue(value=user_id),
-            )
+            ),
         ]
 
         # Add doc_type filter if specified
@@ -123,20 +130,24 @@ class SemanticSearchAlgorithm(SearchAlgorithm):
             top_scores = [p.score for p in search_response.points[:3]]
             logger.debug(f"Top 3 similarity scores: {top_scores}")
 
-        # Deduplicate by (doc_id, doc_type) - multiple chunks per document
-        seen_docs = set()
+        # Deduplicate by (doc_id, doc_type, chunk_start, chunk_end)
+        # This allows multiple chunks from same doc, but removes duplicate chunks
+        seen_chunks = set()
         results = []
 
         for result in search_response.points:
-            doc_id = int(result.payload["doc_id"])
+            # doc_id can be int (notes) or str (files - file paths)
+            doc_id = result.payload["doc_id"]
             doc_type = result.payload.get("doc_type", "note")
-            doc_key = (doc_id, doc_type)
+            chunk_start = result.payload.get("chunk_start_offset")
+            chunk_end = result.payload.get("chunk_end_offset")
+            chunk_key = (doc_id, doc_type, chunk_start, chunk_end)
 
-            # Skip if we've already seen this document
-            if doc_key in seen_docs:
+            # Skip if we've already seen this exact chunk
+            if chunk_key in seen_chunks:
                 continue
 
-            seen_docs.add(doc_key)
+            seen_chunks.add(chunk_key)
 
             # Return unverified results (verification happens at output stage)
             results.append(
@@ -152,6 +163,10 @@ class SemanticSearchAlgorithm(SearchAlgorithm):
                     },
                     chunk_start_offset=result.payload.get("chunk_start_offset"),
                     chunk_end_offset=result.payload.get("chunk_end_offset"),
+                    page_number=result.payload.get("page_number"),
+                    chunk_index=result.payload.get("chunk_index", 0),
+                    total_chunks=result.payload.get("total_chunks", 1),
+                    point_id=str(result.id),  # Qdrant point ID for batch retrieval
                 )
             )
 

nextcloud_mcp_server/server/semantic.py

@@ -26,6 +26,7 @@ from nextcloud_mcp_server.observability.metrics import (
     instrument_tool,
 )
 from nextcloud_mcp_server.search.bm25_hybrid import BM25HybridSearchAlgorithm
+from nextcloud_mcp_server.search.context import get_chunk_with_context
 
 logger = logging.getLogger(__name__)
 
@@ -43,6 +44,8 @@ def configure_semantic_tools(mcp: FastMCP):
         doc_types: list[str] | None = None,
         score_threshold: float = 0.0,
         fusion: str = "rrf",
+        include_context: bool = False,
+        context_chars: int = 300,
     ) -> SemanticSearchResponse:
         """
         Search Nextcloud content using BM25 hybrid search with cross-app support.
@@ -66,6 +69,8 @@ def configure_semantic_tools(mcp: FastMCP):
             fusion: Fusion algorithm: "rrf" (Reciprocal Rank Fusion, default) or "dbsf" (Distribution-Based Score Fusion)
                    RRF: Good general-purpose fusion using reciprocal ranks
                    DBSF: Uses distribution-based normalization, may better balance different score ranges
+            include_context: Whether to expand results with surrounding context (default: False)
+            context_chars: Number of characters to include before/after matched chunk (default: 300)
 
         Returns:
             SemanticSearchResponse with matching documents ranked by fusion scores
@@ -128,18 +133,16 @@ def configure_semantic_tools(mcp: FastMCP):
                 # Sort combined results by score
                 all_results.sort(key=lambda r: r.score, reverse=True)
 
-            # Deduplicate results (hybrid search may return same doc from dense + sparse)
-            # Qdrant already filters by user_id for multi-tenant isolation
-            # Sampling tool will verify access when fetching full content
-            seen = set()
-            unique_results = []
-            for result in all_results:
-                key = (result.id, result.doc_type)
-                if key not in seen:
-                    seen.add(key)
-                    unique_results.append(result)
-
-            search_results = unique_results[:limit]  # Final limit after deduplication
+            # Note: BM25HybridSearchAlgorithm already deduplicates at chunk level
+            # (doc_id, doc_type, chunk_start, chunk_end), which allows multiple
+            # chunks from the same document while preventing duplicate chunks.
+            # No additional deduplication needed here - multiple chunks per document
+            # are valuable for RAG contexts.
+            # Qdrant already filters by user_id for multi-tenant isolation.
+            # Sampling tool will verify access when fetching full content.
+            search_results = all_results[
+                :limit
+            ]  # Final limit after chunk-level dedup in algorithm
 
             # Convert SearchResult objects to SemanticSearchResult for response
             results = []
@@ -160,9 +163,99 @@ def configure_semantic_tools(mcp: FastMCP):
                         else 1,
                         chunk_start_offset=r.chunk_start_offset,
                         chunk_end_offset=r.chunk_end_offset,
+                        page_number=r.page_number,
                     )
                 )
 
+            # Expand results with surrounding context if requested
+            if include_context and results:
+                logger.info(
+                    f"Expanding {len(results)} results with context "
+                    f"(context_chars={context_chars})"
+                )
+
+                # Fetch context for all results in parallel
+                # Limit concurrent requests to prevent connection pool exhaustion
+                max_concurrent = 20
+                semaphore = anyio.Semaphore(max_concurrent)
+                expanded_results = [None] * len(results)
+
+                async def fetch_context(index: int, result: SemanticSearchResult):
+                    """Fetch context for a single result (parallel with semaphore)."""
+                    async with semaphore:
+                        # Only expand if we have valid chunk offsets
+                        if (
+                            result.chunk_start_offset is None
+                            or result.chunk_end_offset is None
+                        ):
+                            # Keep result as-is without context expansion
+                            expanded_results[index] = result
+                            return
+
+                        try:
+                            chunk_context = await get_chunk_with_context(
+                                nc_client=client,
+                                user_id=username,
+                                doc_id=result.id,
+                                doc_type=result.doc_type,
+                                chunk_start=result.chunk_start_offset,
+                                chunk_end=result.chunk_end_offset,
+                                page_number=result.page_number,
+                                chunk_index=result.chunk_index,
+                                total_chunks=result.total_chunks,
+                                context_chars=context_chars,
+                            )
+
+                            if chunk_context:
+                                # Create new result with context fields populated
+                                expanded_results[index] = SemanticSearchResult(
+                                    id=result.id,
+                                    doc_type=result.doc_type,
+                                    title=result.title,
+                                    category=result.category,
+                                    excerpt=result.excerpt,
+                                    score=result.score,
+                                    chunk_index=result.chunk_index,
+                                    total_chunks=result.total_chunks,
+                                    chunk_start_offset=result.chunk_start_offset,
+                                    chunk_end_offset=result.chunk_end_offset,
+                                    page_number=result.page_number,
+                                    # Context expansion fields
+                                    has_context_expansion=True,
+                                    marked_text=chunk_context.marked_text,
+                                    before_context=chunk_context.before_context,
+                                    after_context=chunk_context.after_context,
+                                    has_before_truncation=chunk_context.has_before_truncation,
+                                    has_after_truncation=chunk_context.has_after_truncation,
+                                )
+                                logger.debug(
+                                    f"Expanded context for {result.doc_type} {result.id}"
+                                )
+                            else:
+                                # Context expansion failed, keep original result
+                                expanded_results[index] = result
+                                logger.debug(
+                                    f"Failed to expand context for {result.doc_type} {result.id}, "
+                                    "keeping original result"
+                                )
+                        except Exception as e:
+                            # Context expansion failed, keep original result
+                            expanded_results[index] = result
+                            logger.warning(
+                                f"Error expanding context for {result.doc_type} {result.id}: {e}"
+                            )
+
+                # Run all context fetches in parallel using anyio task group
+                async with anyio.create_task_group() as tg:
+                    for idx, result in enumerate(results):
+                        tg.start_soon(fetch_context, idx, result)
+
+                # Replace results with expanded versions
+                results = [r for r in expanded_results if r is not None]
+                logger.info(
+                    f"Context expansion completed: {len(results)} results with context"
+                )
+
             logger.info(f"Returning {len(results)} results from BM25 hybrid search")
 
             return SemanticSearchResponse(
@@ -202,6 +295,8 @@ def configure_semantic_tools(mcp: FastMCP):
         score_threshold: float = 0.7,
         max_answer_tokens: int = 500,
         fusion: str = "rrf",
+        include_context: bool = False,
+        context_chars: int = 300,
     ) -> SamplingSearchResponse:
         """
         Semantic search with LLM-generated answer using MCP sampling.
@@ -227,6 +322,8 @@ def configure_semantic_tools(mcp: FastMCP):
             score_threshold: Minimum similarity score 0-1 (default: 0.7)
             max_answer_tokens: Maximum tokens for generated answer (default: 500)
             fusion: Fusion algorithm: "rrf" (Reciprocal Rank Fusion, default) or "dbsf" (Distribution-Based Score Fusion)
+            include_context: Whether to expand results with surrounding context (default: False)
+            context_chars: Number of characters to include before/after matched chunk (default: 300)
 
         Returns:
             SamplingSearchResponse containing:
@@ -238,27 +335,6 @@ def configure_semantic_tools(mcp: FastMCP):
         Note: Requires MCP client to support sampling. If sampling is unavailable,
         the tool gracefully degrades to returning documents with an explanation.
         The client may prompt the user to approve the sampling request.
-
-        Examples:
-            >>> # Query about objectives across multiple apps
-            >>> result = await nc_semantic_search_answer(
-            ...     query="What are my Q1 2025 project goals?",
-            ...     ctx=ctx
-            ... )
-            >>> print(result.generated_answer)
-            "Based on Document 1 (note: Project Kickoff), Document 2 (calendar event:
-            Q1 Planning Meeting), and Document 3 (deck card: Implement semantic search),
-            your main goals are: 1) Improve semantic search accuracy by 20%,
-            2) Deploy new embedding model, 3) Reduce indexing latency..."
-
-            >>> # Query about appointments
-            >>> result = await nc_semantic_search_answer(
-            ...     query="When is my next dentist appointment?",
-            ...     ctx=ctx,
-            ...     limit=10
-            ... )
-            >>> len(result.sources)  # Calendar events and related notes
-            3
         """
         # 1. Retrieve relevant documents via existing semantic search
         search_response = await nc_semantic_search(
@@ -267,6 +343,8 @@ def configure_semantic_tools(mcp: FastMCP):
             limit=limit,
             score_threshold=score_threshold,
             fusion=fusion,
+            include_context=include_context,
+            context_chars=context_chars,
         )
 
         # 2. Handle no results case - don't waste a sampling call

nextcloud_mcp_server/server/webdav.py

@@ -64,20 +64,6 @@ def configure_webdav_tools(mcp: FastMCP):
             - Text files are decoded to UTF-8
             - Documents (PDF, DOCX, etc.) are parsed and text is extracted
             - Other binary files are base64 encoded
-
-        Examples:
-            # Read a text file
-            result = await nc_webdav_read_file("Documents/readme.txt")
-            logger.info(result['content'])  # Decoded text content
-
-            # Read a PDF document (automatically parsed)
-            result = await nc_webdav_read_file("Documents/report.pdf")
-            logger.info(result['content'])  # Extracted text from PDF
-            logger.info(result['parsing_metadata'])  # Document parsing info
-
-            # Read a binary file
-            result = await nc_webdav_read_file("Images/photo.jpg")
-            logger.info(result['encoding'])  # 'base64'
         """
         client = await get_client(ctx)
         content, content_type = await client.webdav.read_file(path)

nextcloud_mcp_server/smithery_main.py

@@ -0,0 +1,60 @@
+"""Smithery-specific entrypoint for stateless deployment.
+
+ADR-016: This entrypoint is used when deploying on Smithery's hosting platform.
+It configures the server for stateless operation with per-session authentication.
+
+Features disabled in Smithery mode:
+- Vector sync / semantic search (no persistent storage)
+- Admin UI at /app (no webhooks, no vector viz)
+- OAuth provisioning tools (no token storage)
+
+Features enabled:
+- Core Nextcloud tools (notes, calendar, contacts, files, deck, tables, cookbook)
+- Per-session app password authentication via Smithery configSchema
+- Health check endpoints (/health/live, /health/ready)
+"""
+
+import logging
+import os
+
+import uvicorn
+
+from nextcloud_mcp_server.config import setup_logging
+
+logger = logging.getLogger(__name__)
+
+
+def main():
+    """Start the MCP server in Smithery stateless mode."""
+    # Setup logging first
+    setup_logging()
+
+    # Force stateless mode environment variables
+    os.environ["SMITHERY_DEPLOYMENT"] = "true"
+    os.environ["VECTOR_SYNC_ENABLED"] = "false"
+
+    logger.info("Starting Nextcloud MCP Server in Smithery stateless mode")
+
+    # Import app after setting environment variables
+    from nextcloud_mcp_server.app import get_app
+
+    # Create the app with streamable-http transport (required for Smithery)
+    app = get_app(transport="streamable-http")
+
+    # Smithery sets PORT environment variable
+    port = int(os.environ.get("PORT", 8081))
+
+    logger.info(f"Listening on port {port}")
+
+    uvicorn.run(
+        app,
+        host="0.0.0.0",
+        port=port,
+        log_level="info",
+        # Disable access log for cleaner output
+        access_log=False,
+    )
+
+
+if __name__ == "__main__":
+    main()

nextcloud_mcp_server/vector/document_chunker.py

@@ -15,6 +15,8 @@ class ChunkWithPosition:
     text: str
     start_offset: int  # Character position where chunk starts
     end_offset: int  # Character position where chunk ends (exclusive)
+    page_number: int | None = None  # Page number for PDF chunks (optional)
+    metadata: dict | None = None  # Additional processor-specific metadata (optional)
 
 
 class DocumentChunker:
@@ -50,7 +52,7 @@ class DocumentChunker:
             strip_whitespace=True,
         )
 
-    def chunk_text(self, content: str) -> list[ChunkWithPosition]:
+    async def chunk_text(self, content: str) -> list[ChunkWithPosition]:
         """
         Split text into overlapping chunks with position tracking.
 
@@ -66,12 +68,17 @@ class DocumentChunker:
         Returns:
             List of chunks with their character positions in the original content
         """
+        import anyio
+
         # Handle empty content - return single empty chunk for backward compatibility
         if not content:
             return [ChunkWithPosition(text="", start_offset=0, end_offset=0)]
 
-        # Use LangChain to create documents with position tracking
-        docs = self.splitter.create_documents([content])
+        # Run CPU-bound text splitting in thread pool to avoid blocking event loop
+        docs = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+            self.splitter.create_documents,
+            [content],
+        )
 
         # Convert LangChain Documents to ChunkWithPosition objects
         chunks = [

nextcloud_mcp_server/vector/placeholder.py

@@ -0,0 +1,306 @@
+"""Placeholder point management for Qdrant state tracking.
+
+Placeholders are zero-vector points stored in Qdrant to track document processing
+state. They prevent duplicate work by marking documents as "in-flight" during the
+gap between scanner queuing and processor completion.
+
+Architecture:
+- Scanner writes placeholders when queuing documents for processing
+- Processor deletes placeholders and writes real vectors after processing
+- All user-facing queries filter out placeholders (is_placeholder: False)
+
+Placeholders contain:
+- Zero vectors (dimension from embedding service)
+- is_placeholder: True flag (for filtering)
+- status: "pending", "processing", "completed", "failed"
+- modified_at, etag from source document
+- queued_at timestamp
+"""
+
+import logging
+import time
+import uuid
+
+from qdrant_client.models import FieldCondition, Filter, MatchValue, PointStruct
+
+from nextcloud_mcp_server.config import get_settings
+from nextcloud_mcp_server.embedding import get_embedding_service
+from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
+
+logger = logging.getLogger(__name__)
+
+
+def _generate_placeholder_id(doc_type: str, doc_id: str | int) -> str:
+    """Generate deterministic UUID for placeholder point.
+
+    Args:
+        doc_type: Document type (note, file, etc.)
+        doc_id: Document ID
+
+    Returns:
+        UUID string for point ID
+    """
+    point_name = f"{doc_type}:{doc_id}:placeholder"
+    return str(uuid.uuid5(uuid.NAMESPACE_DNS, point_name))
+
+
+async def write_placeholder_point(
+    doc_id: str | int,
+    doc_type: str,
+    user_id: str,
+    modified_at: int,
+    etag: str = "",
+    file_path: str | None = None,
+) -> None:
+    """Write a placeholder point to Qdrant to mark document as queued.
+
+    This should be called by the scanner BEFORE queuing a document for processing.
+    The placeholder prevents duplicate work if the scanner runs again before
+    processing completes.
+
+    Args:
+        doc_id: Document ID (int for notes/files)
+        doc_type: Document type (note, file, etc.)
+        user_id: User ID who owns the document
+        modified_at: Document modification timestamp
+        etag: Document ETag (if available)
+        file_path: File path (for files only)
+
+    Raises:
+        Exception: If Qdrant write fails
+    """
+    try:
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+        embedding_service = get_embedding_service()
+
+        # Get dimension dynamically (never hardcode)
+        dimension = embedding_service.get_dimension()
+
+        # Create zero vectors
+        zero_dense = [0.0] * dimension
+
+        # Create empty sparse vector for placeholders
+        # Use models.SparseVector with empty indices/values
+        from qdrant_client import models
+
+        empty_sparse = models.SparseVector(indices=[], values=[])
+
+        # Generate deterministic point ID
+        point_id = _generate_placeholder_id(doc_type, doc_id)
+
+        # Build payload
+        payload = {
+            "user_id": user_id,
+            "doc_id": doc_id,
+            "doc_type": doc_type,
+            "is_placeholder": True,
+            "status": "pending",
+            "modified_at": modified_at,
+            "etag": etag,
+            "queued_at": int(time.time()),
+        }
+
+        # Add file_path for files
+        if doc_type == "file" and file_path:
+            payload["file_path"] = file_path
+
+        # Create placeholder point
+        point = PointStruct(
+            id=point_id,
+            vector={
+                "dense": zero_dense,
+                "sparse": empty_sparse,  # Empty sparse vector for placeholders
+            },
+            payload=payload,
+        )
+
+        # Upsert to Qdrant
+        await qdrant_client.upsert(
+            collection_name=settings.get_collection_name(),
+            points=[point],
+            wait=True,
+        )
+
+        logger.debug(
+            f"Wrote placeholder for {doc_type}_{doc_id} (user={user_id}, "
+            f"modified_at={modified_at})"
+        )
+
+    except Exception as e:
+        logger.error(
+            f"Failed to write placeholder for {doc_type}_{doc_id}: {e}",
+            exc_info=True,
+        )
+        raise
+
+
+async def query_document_metadata(
+    doc_id: str | int,
+    doc_type: str,
+    user_id: str,
+) -> dict | None:
+    """Query Qdrant for existing document entry (placeholder or real).
+
+    Returns the payload of the first matching point, which could be:
+    - A placeholder (is_placeholder: True)
+    - A real indexed document (is_placeholder: False or missing)
+    - None if document not in Qdrant
+
+    Args:
+        doc_id: Document ID
+        doc_type: Document type
+        user_id: User ID
+
+    Returns:
+        Payload dict if found, None otherwise
+    """
+    try:
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Query for any entry matching doc_id, doc_type, user_id
+        scroll_result = await qdrant_client.scroll(
+            collection_name=settings.get_collection_name(),
+            scroll_filter=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=doc_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value=doc_type)),
+                ]
+            ),
+            limit=1,
+            with_payload=True,
+            with_vectors=False,
+        )
+
+        if scroll_result[0]:
+            point = scroll_result[0][0]
+            return dict(point.payload)
+
+        return None
+
+    except Exception as e:
+        logger.warning(f"Error querying document metadata for {doc_type}_{doc_id}: {e}")
+        return None
+
+
+async def delete_placeholder_point(
+    doc_id: str | int,
+    doc_type: str,
+    user_id: str,
+) -> None:
+    """Delete a placeholder point from Qdrant.
+
+    This should be called by the processor BEFORE writing real vectors.
+    We delete the placeholder to avoid duplicates, then write the real chunks.
+
+    Args:
+        doc_id: Document ID
+        doc_type: Document type
+        user_id: User ID
+
+    Raises:
+        Exception: If Qdrant delete fails
+    """
+    try:
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Delete by filter (in case there are multiple chunks from old indexing)
+        await qdrant_client.delete(
+            collection_name=settings.get_collection_name(),
+            points_selector=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=doc_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value=doc_type)),
+                    FieldCondition(key="is_placeholder", match=MatchValue(value=True)),
+                ]
+            ),
+        )
+
+        logger.debug(f"Deleted placeholder for {doc_type}_{doc_id} (user={user_id})")
+
+    except Exception as e:
+        logger.error(
+            f"Failed to delete placeholder for {doc_type}_{doc_id}: {e}",
+            exc_info=True,
+        )
+        raise
+
+
+async def update_placeholder_status(
+    doc_id: str | int,
+    doc_type: str,
+    user_id: str,
+    status: str,
+) -> None:
+    """Update the status field of a placeholder point.
+
+    Status values:
+    - "pending": Queued for processing
+    - "processing": Currently being processed
+    - "completed": Processing completed successfully
+    - "failed": Processing failed
+
+    Args:
+        doc_id: Document ID
+        doc_type: Document type
+        user_id: User ID
+        status: New status value
+
+    Raises:
+        Exception: If Qdrant update fails
+    """
+    try:
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
+
+        # Update payload using set_payload
+        await qdrant_client.set_payload(
+            collection_name=settings.get_collection_name(),
+            payload={"status": status},
+            points=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_id", match=MatchValue(value=doc_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value=doc_type)),
+                    FieldCondition(key="is_placeholder", match=MatchValue(value=True)),
+                ]
+            ),
+        )
+
+        logger.debug(
+            f"Updated placeholder status for {doc_type}_{doc_id} to '{status}' "
+            f"(user={user_id})"
+        )
+
+    except Exception as e:
+        logger.warning(
+            f"Failed to update placeholder status for {doc_type}_{doc_id}: {e}"
+        )
+        # Don't raise - status updates are non-critical
+
+
+def get_placeholder_filter() -> FieldCondition:
+    """Get a filter condition to exclude placeholders from queries.
+
+    Add this to all user-facing search/visualization queries to ensure
+    placeholders are never returned to users.
+
+    Returns:
+        FieldCondition that filters out is_placeholder: True
+
+    Example:
+        Filter(
+            must=[
+                get_placeholder_filter(),  # Exclude placeholders
+                FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+            ]
+        )
+    """
+    return FieldCondition(
+        key="is_placeholder",
+        match=MatchValue(value=False),
+    )

nextcloud_mcp_server/vector/processor.py

@@ -23,12 +23,50 @@ from nextcloud_mcp_server.observability.metrics import (
 )
 from nextcloud_mcp_server.observability.tracing import trace_operation
 from nextcloud_mcp_server.vector.document_chunker import DocumentChunker
+from nextcloud_mcp_server.vector.placeholder import delete_placeholder_point
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 from nextcloud_mcp_server.vector.scanner import DocumentTask
 
 logger = logging.getLogger(__name__)
 
 
+def assign_page_numbers(chunks, page_boundaries):
+    """Assign page numbers to chunks based on page boundaries.
+
+    Each chunk gets the page number where most of its content appears.
+    For chunks spanning multiple pages, assigns the page containing the
+    majority of the chunk's characters.
+
+    Args:
+        chunks: List of ChunkWithPosition objects
+        page_boundaries: List of dicts with {page, start_offset, end_offset}
+
+    Returns:
+        None (modifies chunks in place)
+    """
+    if not page_boundaries:
+        return
+
+    for chunk in chunks:
+        # Find which page(s) this chunk overlaps with
+        max_overlap = 0
+        assigned_page = None
+
+        for boundary in page_boundaries:
+            # Calculate overlap between chunk and page
+            overlap_start = max(chunk.start_offset, boundary["start_offset"])
+            overlap_end = min(chunk.end_offset, boundary["end_offset"])
+            overlap = max(0, overlap_end - overlap_start)
+
+            # Assign to page with maximum overlap
+            if overlap > max_overlap:
+                max_overlap = overlap
+                assigned_page = boundary["page"]
+
+        if assigned_page is not None:
+            chunk.page_number = assigned_page
+
+
 async def processor_task(
     worker_id: int,
     receive_stream: MemoryObjectReceiveStream[DocumentTask],
@@ -218,31 +256,265 @@ async def _index_document(
     settings = get_settings()
 
     # Fetch document content
-    if doc_task.doc_type == "note":
-        document = await nc_client.notes.get_note(int(doc_task.doc_id))
-        content = f"{document['title']}\n\n{document['content']}"
-        title = document["title"]
-        etag = document.get("etag", "")
-    else:
-        raise ValueError(f"Unsupported doc_type: {doc_task.doc_type}")
+    with trace_operation(
+        "vector_sync.fetch_content",
+        attributes={
+            "vector_sync.doc_type": doc_task.doc_type,
+            "vector_sync.doc_id": doc_task.doc_id,
+        },
+    ):
+        if doc_task.doc_type == "note":
+            document = await nc_client.notes.get_note(int(doc_task.doc_id))
+            content = f"{document['title']}\n\n{document['content']}"
+            title = document["title"]
+            etag = document.get("etag", "")
+            file_metadata = {}  # No file-specific metadata for notes
+            file_path = None  # Notes don't have file paths
+            content_bytes = None  # Notes don't have binary content
+            content_type = None
+        elif doc_task.doc_type == "file":
+            # For files, doc_id is now the numeric file ID, file_path comes from DocumentTask
+            if not doc_task.file_path:
+                raise ValueError(
+                    f"File path required for file indexing but not provided (file_id={doc_task.doc_id})"
+                )
+            file_path = doc_task.file_path
+
+            # Read file content via WebDAV
+            content_bytes, content_type = await nc_client.webdav.read_file(file_path)
+        else:
+            raise ValueError(f"Unsupported doc_type: {doc_task.doc_type}")
+
+    # Process file content (text extraction)
+    if doc_task.doc_type == "file":
+        # Type narrowing: content_bytes and content_type are set for files
+        assert content_bytes is not None
+        assert content_type is not None
+        assert file_path is not None
+
+        with trace_operation(
+            "vector_sync.document_process",
+            attributes={
+                "vector_sync.content_type": content_type,
+                "vector_sync.file_size": len(content_bytes),
+            },
+        ):
+            # Use document processor registry to extract text
+            from nextcloud_mcp_server.document_processors import get_registry
+
+            registry = get_registry()
+
+            try:
+                result = await registry.process(
+                    content=content_bytes,
+                    content_type=content_type,
+                    filename=file_path,
+                )
+                content = result.text
+                file_metadata = result.metadata
+                title = file_metadata.get("title") or file_path.split("/")[-1]
+                etag = ""  # WebDAV read_file doesn't return etag
+
+                # Diagnostic: Log page boundary information if available
+                if "page_boundaries" in file_metadata:
+                    page_boundaries = file_metadata["page_boundaries"]
+                    logger.info(
+                        f"Page boundaries for {file_path}: "
+                        f"{len(page_boundaries)} pages, text length: {len(content)}"
+                    )
+                    # Log first 3 page boundaries for debugging
+                    for boundary in page_boundaries[:3]:
+                        logger.debug(
+                            f"  Page {boundary['page']}: "
+                            f"offsets [{boundary['start_offset']}:{boundary['end_offset']}]"
+                        )
+                    # Verify last boundary matches text length
+                    if page_boundaries:
+                        last_boundary = page_boundaries[-1]
+                        if last_boundary["end_offset"] != len(content):
+                            logger.warning(
+                                f"Text length mismatch: content={len(content)}, "
+                                f"last_boundary_end={last_boundary['end_offset']}"
+                            )
+                else:
+                    logger.debug(f"No page_boundaries in metadata for {file_path}")
+            except Exception as e:
+                logger.error(f"Failed to process file {file_path}: {e}")
+                raise
 
     # Tokenize and chunk (using configured chunk size and overlap)
-    chunker = DocumentChunker(
-        chunk_size=settings.document_chunk_size,
-        overlap=settings.document_chunk_overlap,
-    )
-    chunks = chunker.chunk_text(content)
+    with trace_operation(
+        "vector_sync.chunk_text",
+        attributes={
+            "vector_sync.input_chars": len(content),
+            "vector_sync.chunk_size": settings.document_chunk_size,
+            "vector_sync.overlap": settings.document_chunk_overlap,
+        },
+    ):
+        chunker = DocumentChunker(
+            chunk_size=settings.document_chunk_size,
+            overlap=settings.document_chunk_overlap,
+        )
+        chunks = await chunker.chunk_text(content)
+
+    # Assign page numbers to chunks if page boundaries are available (PDFs)
+    if doc_task.doc_type == "file" and "page_boundaries" in file_metadata:
+        with trace_operation(
+            "vector_sync.assign_page_numbers",
+            attributes={
+                "vector_sync.chunk_count": len(chunks),
+                "vector_sync.page_count": len(file_metadata["page_boundaries"]),
+            },
+        ):
+            assign_page_numbers(chunks, file_metadata["page_boundaries"])
+
+            # Diagnostic: Verify page number assignment
+            assigned_count = sum(1 for c in chunks if c.page_number is not None)
+            logger.info(
+                f"Assigned page numbers to {assigned_count}/{len(chunks)} chunks "
+                f"for {file_path}"
+            )
+
+            # Log first 3 chunks to see their page assignments
+            for i, chunk in enumerate(chunks[:3]):
+                logger.debug(
+                    f"  Chunk {i}: page={chunk.page_number}, "
+                    f"offsets=[{chunk.start_offset}:{chunk.end_offset}]"
+                )
+
+            # Warning if NO page numbers were assigned
+            if assigned_count == 0:
+                logger.warning(
+                    f"NO page numbers assigned! "
+                    f"Text length: {len(content)}, "
+                    f"Chunks: {len(chunks)}, "
+                    f"Chunk offset range: [{chunks[0].start_offset}:{chunks[-1].end_offset}], "
+                    f"Page boundaries: {len(file_metadata['page_boundaries'])} pages, "
+                    f"First boundary: {file_metadata['page_boundaries'][0] if file_metadata['page_boundaries'] else 'None'}"
+                )
 
     # Extract chunk texts for embedding
     chunk_texts = [chunk.text for chunk in chunks]
 
-    # Generate dense embeddings (I/O bound - external API call)
-    embedding_service = get_embedding_service()
-    dense_embeddings = await embedding_service.embed_batch(chunk_texts)
+    # Initialize results containers
+    dense_embeddings: list = []
+    sparse_embeddings: list = []
+    chunk_images: dict[int, dict] = {}
 
-    # Generate sparse embeddings (BM25 for keyword matching)
-    bm25_service = get_bm25_service()
-    sparse_embeddings = bm25_service.encode_batch(chunk_texts)
+    # Determine if we need PDF highlighting
+    is_pdf = doc_task.doc_type == "file" and content_type == "application/pdf"
+
+    # Define async tasks for parallel execution
+    async def generate_dense_embeddings():
+        """Generate dense embeddings (I/O bound - external API call)."""
+        nonlocal dense_embeddings
+        with trace_operation(
+            "vector_sync.embed_dense",
+            attributes={
+                "vector_sync.chunk_count": len(chunk_texts),
+                "vector_sync.total_chars": sum(len(t) for t in chunk_texts),
+            },
+        ):
+            embedding_service = get_embedding_service()
+            dense_embeddings = await embedding_service.embed_batch(chunk_texts)
+
+    async def generate_sparse_embeddings():
+        """Generate sparse embeddings (BM25 for keyword matching)."""
+        nonlocal sparse_embeddings
+        with trace_operation(
+            "vector_sync.embed_sparse",
+            attributes={
+                "vector_sync.chunk_count": len(chunk_texts),
+            },
+        ):
+            bm25_service = get_bm25_service()
+            sparse_embeddings = await bm25_service.encode_batch(chunk_texts)
+
+    async def generate_highlights():
+        """Generate highlighted page images for PDF chunks (CPU-bound)."""
+        nonlocal chunk_images
+        if not is_pdf:
+            return
+
+        # Type narrowing: content_bytes is set for PDF files
+        assert content_bytes is not None
+
+        with trace_operation(
+            "vector_sync.generate_highlights",
+            attributes={
+                "vector_sync.chunk_count": len(chunks),
+                "vector_sync.pdf_size": len(content_bytes),
+            },
+        ):
+            import base64
+
+            from nextcloud_mcp_server.search.pdf_highlighter import PDFHighlighter
+
+            # Build chunk data for batch processing
+            # Format: (chunk_index, start_offset, end_offset, page_number, chunk_text)
+            chunk_data: list[tuple[int, int, int, int | None, str]] = [
+                (i, chunk.start_offset, chunk.end_offset, chunk.page_number, chunk.text)
+                for i, chunk in enumerate(chunks)
+                if chunk.page_number is not None
+            ]
+
+            # Get pre-computed page boundaries from document processor
+            page_boundaries = file_metadata.get("page_boundaries")
+            if not page_boundaries:
+                logger.warning("No page boundaries available, skipping highlighting")
+                return
+
+            logger.info(
+                f"Batch generating highlighted page images for {len(chunk_data)} PDF chunks"
+            )
+
+            # Run CPU-bound highlighting in thread pool
+            # Pass pre-computed page boundaries and full text to avoid re-processing the PDF
+            batch_results = await anyio.to_thread.run_sync(  # type: ignore[attr-defined]
+                lambda: PDFHighlighter.highlight_chunks_batch(
+                    pdf_bytes=content_bytes,
+                    chunks=chunk_data,
+                    page_boundaries=page_boundaries,
+                    full_text=content,
+                    color="yellow",
+                    zoom=2.0,
+                )
+            )
+
+            # Convert results to storage format
+            for chunk_index, (
+                png_bytes,
+                actual_page_num,
+                highlight_count,
+            ) in batch_results.items():
+                image_base64 = base64.b64encode(png_bytes).decode("utf-8")
+                chunk_images[chunk_index] = {
+                    "image": image_base64,
+                    "page": actual_page_num,
+                    "highlights": highlight_count,
+                    "size": len(png_bytes),
+                }
+
+            logger.info(
+                f"Generated {len(chunk_images)}/{len(chunks)} highlighted page images "
+                f"(avg {sum(img['size'] for img in chunk_images.values()) // max(len(chunk_images), 1):,} bytes)"
+            )
+
+    # Run all embedding/highlighting operations in parallel
+    # - Dense embeddings: I/O bound (API call)
+    # - Sparse embeddings: CPU bound (local BM25)
+    # - Highlighting: CPU bound (PyMuPDF rendering, runs in thread pool)
+    with trace_operation(
+        "vector_sync.parallel_processing",
+        attributes={
+            "vector_sync.is_pdf": is_pdf,
+            "vector_sync.chunk_count": len(chunks),
+        },
+    ):
+        async with anyio.create_task_group() as tg:
+            tg.start_soon(generate_dense_embeddings)
+            tg.start_soon(generate_sparse_embeddings)
+            tg.start_soon(generate_highlights)
 
     # Prepare Qdrant points
     indexed_at = int(time.time())
@@ -267,8 +539,9 @@ async def _index_document(
                     "user_id": doc_task.user_id,
                     "doc_id": doc_task.doc_id,
                     "doc_type": doc_task.doc_type,
+                    "is_placeholder": False,  # Real indexed document (not placeholder)
                     "title": title,
-                    "excerpt": chunk.text[:200],
+                    "excerpt": chunk.text,  # Full chunk text (up to chunk_size, default 2048 chars)
                     "indexed_at": indexed_at,
                     "modified_at": doc_task.modified_at,
                     "etag": etag,
@@ -277,16 +550,74 @@ async def _index_document(
                     "chunk_start_offset": chunk.start_offset,
                     "chunk_end_offset": chunk.end_offset,
                     "metadata_version": 2,  # v2 includes position metadata
+                    # File-specific metadata (PDF, etc.)
+                    **(
+                        {
+                            "file_path": file_path,  # Store file path for retrieval
+                            "mime_type": content_type,  # From WebDAV response
+                            "file_size": file_metadata.get("file_size"),
+                            "page_number": chunk.page_number,
+                            "page_count": file_metadata.get("page_count"),
+                            "author": file_metadata.get("author"),
+                            "creation_date": file_metadata.get("creation_date"),
+                            "has_images": file_metadata.get("has_images", False),
+                            "image_count": file_metadata.get("image_count", 0),
+                        }
+                        if doc_task.doc_type == "file"
+                        else {}
+                    ),
+                    # Highlighted page image (PDF only)
+                    **(
+                        {
+                            "highlighted_page_image": chunk_images[i]["image"],
+                            "highlighted_page_number": chunk_images[i]["page"],
+                            "highlight_count": chunk_images[i]["highlights"],
+                        }
+                        if i in chunk_images
+                        else {}
+                    ),
                 },
             )
         )
 
-    # Upsert to Qdrant
-    await qdrant_client.upsert(
-        collection_name=settings.get_collection_name(),
-        points=points,
-        wait=True,
-    )
+    # Delete placeholder before writing real vectors
+    # This prevents duplicates and cleans up the placeholder state
+    try:
+        await delete_placeholder_point(
+            doc_id=doc_task.doc_id,
+            doc_type=doc_task.doc_type,
+            user_id=doc_task.user_id,
+        )
+    except Exception as e:
+        # Log but don't fail indexing if placeholder deletion fails
+        logger.warning(
+            f"Failed to delete placeholder for {doc_task.doc_type}_{doc_task.doc_id}: {e}"
+        )
+
+    # Upsert to Qdrant in batches to avoid timeout with large payloads
+    # Each batch is limited to avoid WriteTimeout when sending large image payloads
+    BATCH_SIZE = 10  # ~2MB per batch with images
+    with trace_operation(
+        "vector_sync.qdrant_upsert",
+        attributes={
+            "vector_sync.point_count": len(points),
+            "vector_sync.collection": settings.get_collection_name(),
+            "vector_sync.images_count": len(chunk_images),
+            "vector_sync.batch_size": BATCH_SIZE,
+        },
+    ):
+        for batch_start in range(0, len(points), BATCH_SIZE):
+            batch_end = min(batch_start + BATCH_SIZE, len(points))
+            batch = points[batch_start:batch_end]
+            await qdrant_client.upsert(
+                collection_name=settings.get_collection_name(),
+                points=batch,
+                wait=True,
+            )
+            if batch_end < len(points):
+                logger.debug(
+                    f"Upserted batch {batch_start // BATCH_SIZE + 1}/{(len(points) + BATCH_SIZE - 1) // BATCH_SIZE}"
+                )
 
     logger.info(
         f"Indexed {doc_task.doc_type}_{doc_task.doc_id} for {doc_task.user_id} "

nextcloud_mcp_server/vector/scanner.py

@@ -4,6 +4,7 @@ Periodically scans enabled users' content and queues changed documents for proce
 """
 
 import logging
+import os
 import time
 from dataclasses import dataclass
 
@@ -16,6 +17,10 @@ from nextcloud_mcp_server.client import NextcloudClient
 from nextcloud_mcp_server.config import get_settings
 from nextcloud_mcp_server.observability.metrics import record_vector_sync_scan
 from nextcloud_mcp_server.observability.tracing import trace_operation
+from nextcloud_mcp_server.vector.placeholder import (
+    query_document_metadata,
+    write_placeholder_point,
+)
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
 logger = logging.getLogger(__name__)
@@ -26,10 +31,11 @@ class DocumentTask:
     """Document task for processing queue."""
 
     user_id: str
-    doc_id: str
+    doc_id: int | str  # int for files/notes, str for legacy
     doc_type: str  # "note", "file", "calendar"
     operation: str  # "index" or "delete"
     modified_at: int
+    file_path: str | None = None  # File path for files (when doc_id is file_id)
 
 
 # Track documents potentially deleted (grace period before actual deletion)
@@ -182,8 +188,9 @@ async def scan_user_documents(
                 f"[SCAN-{scan_id}] Using pruneBefore={prune_before} to optimize data transfer"
             )
 
-        # Get indexed state from Qdrant first (for incremental sync)
-        indexed_docs = {}
+        # For deletion tracking, get all doc_ids in Qdrant (for incremental sync)
+        # Note: We no longer bulk-query indexed_at, instead check per-document
+        indexed_doc_ids = set()
         if not initial_sync:
             qdrant_client = await get_qdrant_client()
             scroll_result = await qdrant_client.scroll(
@@ -194,17 +201,14 @@ async def scan_user_documents(
                         FieldCondition(key="doc_type", match=MatchValue(value="note")),
                     ]
                 ),
-                with_payload=["doc_id", "indexed_at"],
+                with_payload=["doc_id"],
                 with_vectors=False,
                 limit=10000,
             )
 
-            indexed_docs = {
-                point.payload["doc_id"]: point.payload["indexed_at"]
-                for point in scroll_result[0]
-            }
+            indexed_doc_ids = {point.payload["doc_id"] for point in scroll_result[0]}
 
-            logger.debug(f"Found {len(indexed_docs)} indexed documents in Qdrant")
+            logger.debug(f"Found {len(indexed_doc_ids)} indexed documents in Qdrant")
 
         # Stream notes from Nextcloud and process immediately
         note_count = 0
@@ -218,7 +222,14 @@ async def scan_user_documents(
             modified_at = note.get("modified", 0)
 
             if initial_sync:
-                # Send everything on first sync
+                # Send everything on first sync - write placeholder first
+                await write_placeholder_point(
+                    doc_id=doc_id,
+                    doc_type="note",
+                    user_id=user_id,
+                    modified_at=modified_at,
+                    etag=note.get("etag", ""),
+                )
                 await send_stream.send(
                     DocumentTask(
                         user_id=user_id,
@@ -230,9 +241,7 @@ async def scan_user_documents(
                 )
                 queued += 1
             else:
-                # Incremental sync: compare with indexed state
-                indexed_at = indexed_docs.get(doc_id)
-
+                # Incremental sync: check if document exists and compare modified_at
                 # If document reappeared, remove from potentially_deleted
                 doc_key = (user_id, doc_id)
                 if doc_key in _potentially_deleted:
@@ -241,8 +250,48 @@ async def scan_user_documents(
                     )
                     del _potentially_deleted[doc_key]
 
+                # Query Qdrant for existing entry (placeholder or real)
+                existing_metadata = await query_document_metadata(
+                    doc_id=doc_id, doc_type="note", user_id=user_id
+                )
+
                 # Send if never indexed or modified since last index
-                if indexed_at is None or modified_at > indexed_at:
+                # Compare against stored modified_at (not indexed_at!)
+                needs_indexing = False
+                if existing_metadata is None:
+                    # Never seen before
+                    needs_indexing = True
+                elif existing_metadata.get("modified_at", 0) < modified_at:
+                    # Document modified since last indexing
+                    needs_indexing = True
+                elif existing_metadata.get("is_placeholder", False):
+                    # Placeholder exists - check if it's stale (processing may have failed)
+                    # Only requeue if placeholder is older than 5x scan interval
+                    # (Large PDFs can take 3-4 minutes to process)
+                    queued_at = existing_metadata.get("queued_at", 0)
+                    placeholder_age = time.time() - queued_at
+                    stale_threshold = get_settings().vector_sync_scan_interval * 5
+                    if placeholder_age > stale_threshold:
+                        logger.debug(
+                            f"Found stale placeholder for note {doc_id} "
+                            f"(age={placeholder_age:.1f}s), requeuing"
+                        )
+                        needs_indexing = True
+                    else:
+                        logger.debug(
+                            f"Skipping note {doc_id} with recent placeholder "
+                            f"(age={placeholder_age:.1f}s < {stale_threshold:.1f}s)"
+                        )
+
+                if needs_indexing:
+                    # Write placeholder before queuing
+                    await write_placeholder_point(
+                        doc_id=doc_id,
+                        doc_type="note",
+                        user_id=user_id,
+                        modified_at=modified_at,
+                        etag=note.get("etag", ""),
+                    )
                     await send_stream.send(
                         DocumentTask(
                             user_id=user_id,
@@ -270,7 +319,7 @@ async def scan_user_documents(
         )  # Allow 1.5 scan intervals
         current_time = time.time()
 
-        for doc_id in indexed_docs:
+        for doc_id in indexed_doc_ids:
             if doc_id not in nextcloud_doc_ids:
                 doc_key = (user_id, doc_id)
 
@@ -309,7 +358,195 @@ async def scan_user_documents(
                     )
                     _potentially_deleted[doc_key] = current_time
 
+        # Scan tagged PDF files (after notes)
+        # Get indexed file IDs from Qdrant (for deletion tracking)
+        indexed_file_ids = set()
+        if not initial_sync:
+            file_scroll_result = await qdrant_client.scroll(
+                collection_name=settings.get_collection_name(),
+                scroll_filter=Filter(
+                    must=[
+                        FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                        FieldCondition(key="doc_type", match=MatchValue(value="file")),
+                    ]
+                ),
+                limit=10000,  # Reasonable limit for file count
+                with_payload=["doc_id"],
+                with_vectors=False,
+            )
+
+            indexed_file_ids = {
+                point.payload["doc_id"] for point in file_scroll_result[0]
+            }
+
+            logger.debug(f"Found {len(indexed_file_ids)} indexed files in Qdrant")
+
+        # Scan for tagged PDF files
+        file_count = 0
+        file_queued = 0
+        nextcloud_file_ids = set()
+
+        try:
+            # Find files with vector-index tag using OCS Tags API
+            settings = get_settings()
+            tag_name = os.getenv("VECTOR_SYNC_PDF_TAG", "vector-index")
+            # Use NextcloudClient.find_files_by_tag() which uses proper OCS API
+            # and filters by PDF MIME type
+            tagged_files = await nc_client.find_files_by_tag(
+                tag_name, mime_type_filter="application/pdf"
+            )
+
+            for file_info in tagged_files:
+                # Files are already filtered by MIME type in find_files_by_tag()
+                file_count += 1
+                file_id = file_info["id"]  # Use numeric file ID, not path
+                file_path = file_info["path"]  # Keep path for logging
+                nextcloud_file_ids.add(file_id)
+
+                # Use last_modified timestamp if available, otherwise use current time
+                modified_at = file_info.get("last_modified_timestamp", int(time.time()))
+                if isinstance(file_info.get("last_modified"), str):
+                    # Parse RFC 2822 date format if needed
+                    from email.utils import parsedate_to_datetime
+
+                    try:
+                        dt = parsedate_to_datetime(file_info["last_modified"])
+                        modified_at = int(dt.timestamp())
+                    except (ValueError, KeyError):
+                        pass
+
+                if initial_sync:
+                    # Send everything on first sync - write placeholder first
+                    await write_placeholder_point(
+                        doc_id=file_id,
+                        doc_type="file",
+                        user_id=user_id,
+                        modified_at=modified_at,
+                        file_path=file_path,
+                    )
+                    await send_stream.send(
+                        DocumentTask(
+                            user_id=user_id,
+                            doc_id=file_id,  # Use numeric file ID
+                            doc_type="file",
+                            operation="index",
+                            modified_at=modified_at,
+                            file_path=file_path,  # Pass file path for content retrieval
+                        )
+                    )
+                    file_queued += 1
+                else:
+                    # Incremental sync: check if file exists and compare modified_at
+                    # If file reappeared, remove from potentially_deleted
+                    file_key = (user_id, file_id)
+                    if file_key in _potentially_deleted:
+                        logger.debug(
+                            f"File {file_path} (ID: {file_id}) reappeared, removing from deletion grace period"
+                        )
+                        del _potentially_deleted[file_key]
+
+                    # Query Qdrant for existing entry (placeholder or real)
+                    existing_metadata = await query_document_metadata(
+                        doc_id=file_id, doc_type="file", user_id=user_id
+                    )
+
+                    # Send if never indexed or modified since last index
+                    # Compare against stored modified_at (not indexed_at!)
+                    needs_indexing = False
+                    if existing_metadata is None:
+                        # Never seen before
+                        needs_indexing = True
+                    elif existing_metadata.get("modified_at", 0) < modified_at:
+                        # File modified since last indexing
+                        needs_indexing = True
+                    elif existing_metadata.get("is_placeholder", False):
+                        # Placeholder exists - check if it's stale (processing may have failed)
+                        # Only requeue if placeholder is older than 5x scan interval
+                        # (Large PDFs can take 3-4 minutes to process)
+                        queued_at = existing_metadata.get("queued_at", 0)
+                        placeholder_age = time.time() - queued_at
+                        stale_threshold = get_settings().vector_sync_scan_interval * 5
+                        if placeholder_age > stale_threshold:
+                            logger.debug(
+                                f"Found stale placeholder for file {file_path} (ID: {file_id}) "
+                                f"(age={placeholder_age:.1f}s), requeuing"
+                            )
+                            needs_indexing = True
+                        else:
+                            logger.debug(
+                                f"Skipping file {file_path} (ID: {file_id}) with recent placeholder "
+                                f"(age={placeholder_age:.1f}s < {stale_threshold:.1f}s)"
+                            )
+
+                    if needs_indexing:
+                        # Write placeholder before queuing
+                        await write_placeholder_point(
+                            doc_id=file_id,
+                            doc_type="file",
+                            user_id=user_id,
+                            modified_at=modified_at,
+                            file_path=file_path,
+                        )
+                        await send_stream.send(
+                            DocumentTask(
+                                user_id=user_id,
+                                doc_id=file_id,  # Use numeric file ID
+                                doc_type="file",
+                                operation="index",
+                                modified_at=modified_at,
+                                file_path=file_path,  # Pass file path for content retrieval
+                            )
+                        )
+                        file_queued += 1
+
+            logger.info(
+                f"[SCAN-{scan_id}] Found {file_count} tagged PDFs for {user_id}"
+            )
+            record_vector_sync_scan(file_count)
+
+            # Check for deleted files (not initial sync)
+            if not initial_sync:
+                for file_id in indexed_file_ids:
+                    if file_id not in nextcloud_file_ids:
+                        file_key = (user_id, file_id)
+
+                        if file_key in _potentially_deleted:
+                            # Check if grace period elapsed
+                            first_missing_time = _potentially_deleted[file_key]
+                            time_missing = current_time - first_missing_time
+
+                            if time_missing >= grace_period:
+                                # Grace period elapsed, send for deletion
+                                logger.info(
+                                    f"File ID {file_id} missing for {time_missing:.1f}s "
+                                    f"(>{grace_period:.1f}s grace period), sending deletion"
+                                )
+                                await send_stream.send(
+                                    DocumentTask(
+                                        user_id=user_id,
+                                        doc_id=file_id,  # Use numeric file ID
+                                        doc_type="file",
+                                        operation="delete",
+                                        modified_at=0,
+                                    )
+                                )
+                                file_queued += 1
+                                del _potentially_deleted[file_key]
+                        else:
+                            # First time missing, add to grace period tracking
+                            logger.debug(
+                                f"File ID {file_id} missing for first time, starting grace period"
+                            )
+                            _potentially_deleted[file_key] = current_time
+
+        except Exception as e:
+            logger.warning(f"Failed to scan tagged files for {user_id}: {e}")
+
+        queued += file_queued
+
         if queued > 0:
-            logger.info(f"Sent {queued} documents for incremental sync: {user_id}")
+            logger.info(
+                f"Sent {queued} documents ({file_queued} files) for incremental sync: {user_id}"
+            )
         else:
             logger.debug(f"No changes detected for {user_id}")

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "nextcloud-mcp-server"
-version = "0.44.0"
+version = "0.46.2"
 description = "Model Context Protocol (MCP) server for Nextcloud integration - enables AI assistants to interact with Nextcloud data"
 authors = [
     {name = "Chris Coutinho", email = "chris@coutinho.io"}
@@ -10,7 +10,7 @@ license = {text = "AGPL-3.0-only"}
 requires-python = ">=3.11"
 keywords = ["nextcloud", "mcp", "model-context-protocol", "llm", "ai", "claude", "webdav", "caldav", "carddav"]
 dependencies = [
-    "mcp[cli] (>=1.21,<1.22)",
+    "mcp[cli] (>=1.22,<1.23)",
     "httpx (>=0.28.1,<0.29.0)",
     "pillow (>=10.3.0,<12.0.0)", # Compatible with fastembed
     "icalendar (>=6.0.0,<7.0.0)",
@@ -36,6 +36,9 @@ dependencies = [
     "python-json-logger>=3.2.0", # Structured JSON logging
     "jinja2>=3.1.6",
     "langchain-text-splitters>=1.0.0",
+    "pymupdf>=1.26.6",
+    "pymupdf4llm>=0.2.2",
+    "pymupdf-layout>=1.26.6",
 ]
 classifiers = [
     "Development Status :: 4 - Beta",
@@ -123,6 +126,7 @@ dev = [
 
 [project.scripts]
 nextcloud-mcp-server = "nextcloud_mcp_server.cli:run"
+smithery-main = "nextcloud_mcp_server.smithery_main:main"
 
 [[tool.uv.index]]
 name = "testpypi"

smithery.yaml

@@ -0,0 +1,38 @@
+# Smithery configuration for Nextcloud MCP Server
+# See: https://smithery.ai/docs/build/configuration
+# ADR-016: Stateless deployment mode for multi-user public Nextcloud instances
+
+runtime: "container"
+
+build:
+  dockerfile: "Dockerfile.smithery"
+  dockerBuildPath: "."
+
+startCommand:
+  type: "http"
+  configSchema:
+    type: "object"
+    required:
+      - "nextcloud_url"
+      - "username"
+      - "app_password"
+    properties:
+      nextcloud_url:
+        type: "string"
+        title: "Nextcloud URL"
+        description: "Your Nextcloud instance URL (e.g., https://cloud.example.com). Must be publicly accessible."
+        pattern: "^https?://.+"
+      username:
+        type: "string"
+        title: "Username"
+        description: "Your Nextcloud username"
+        minLength: 1
+      app_password:
+        type: "string"
+        title: "App Password"
+        description: "Nextcloud app password. Generate at Settings > Security > App passwords. Do NOT use your main password."
+        minLength: 1
+  exampleConfig:
+    nextcloud_url: "https://cloud.example.com"
+    username: "alice"
+    app_password: "xxxxx-xxxxx-xxxxx-xxxxx-xxxxx"

tests/integration/test_pdf_indexing.py

@@ -0,0 +1,361 @@
+"""Integration tests for PDF document indexing and semantic search.
+
+These tests validate the complete PDF processing flow:
+1. Process PDF with PyMuPDFProcessor
+2. Chunk extracted text with page numbers
+3. Index chunks into Qdrant with metadata
+4. Perform semantic search on PDF content
+5. Verify page numbers and metadata are preserved
+"""
+
+import pymupdf
+import pytest
+from qdrant_client import AsyncQdrantClient
+from qdrant_client.models import Distance, PointStruct, VectorParams
+
+from nextcloud_mcp_server.document_processors.pymupdf import PyMuPDFProcessor
+from nextcloud_mcp_server.embedding import SimpleEmbeddingProvider
+from nextcloud_mcp_server.vector.document_chunker import (
+    ChunkWithPosition,
+    RecursiveCharacterTextSplitter,
+)
+
+pytestmark = pytest.mark.integration
+
+
+def create_test_pdf() -> bytes:
+    """Create a small test PDF with multiple pages."""
+    doc = pymupdf.open()
+
+    # Page 1: Introduction
+    page1 = doc.new_page(width=595, height=842)  # A4 size
+    page1.insert_text(
+        (50, 50),
+        "Nextcloud Administration Guide\n\n"
+        "Chapter 1: Introduction\n\n"
+        "Nextcloud is a self-hosted file sharing and collaboration platform. "
+        "It provides secure file storage, sharing, and synchronization across devices. "
+        "This guide covers installation, configuration, and maintenance of Nextcloud.",
+    )
+
+    # Page 2: Installation
+    page2 = doc.new_page(width=595, height=842)
+    page2.insert_text(
+        (50, 50),
+        "Chapter 2: Installation\n\n"
+        "System Requirements:\n"
+        "- PHP 8.0 or higher\n"
+        "- MySQL 8.0 or MariaDB 10.5\n"
+        "- Apache or Nginx web server\n\n"
+        "Installation steps:\n"
+        "1. Download Nextcloud package\n"
+        "2. Extract to web server directory\n"
+        "3. Configure database connection\n"
+        "4. Run installation wizard",
+    )
+
+    # Page 3: Configuration
+    page3 = doc.new_page(width=595, height=842)
+    page3.insert_text(
+        (50, 50),
+        "Chapter 3: Configuration\n\n"
+        "Database Configuration:\n"
+        "Edit config/config.php to set database parameters. "
+        "Configure database host, username, password, and database name. "
+        "For optimal performance, use MySQL or MariaDB.\n\n"
+        "Security Settings:\n"
+        "Enable HTTPS, configure trusted domains, and set up firewall rules.",
+    )
+
+    # Convert to bytes
+    pdf_bytes = doc.tobytes()
+    doc.close()
+
+    return pdf_bytes
+
+
+@pytest.fixture
+async def simple_embedding_provider():
+    """Simple in-process embedding provider for testing."""
+    return SimpleEmbeddingProvider(dimension=384)
+
+
+@pytest.fixture
+async def qdrant_test_client():
+    """Qdrant client for testing (in-memory)."""
+    client = AsyncQdrantClient(":memory:")
+    yield client
+    await client.close()
+
+
+@pytest.fixture
+async def test_collection(qdrant_test_client: AsyncQdrantClient):
+    """Create test collection in Qdrant."""
+    collection_name = "test_pdf_indexing"
+
+    # Create collection
+    await qdrant_test_client.create_collection(
+        collection_name=collection_name,
+        vectors_config=VectorParams(size=384, distance=Distance.COSINE),
+    )
+
+    yield collection_name
+
+    # Cleanup
+    try:
+        await qdrant_test_client.delete_collection(collection_name)
+    except Exception:
+        pass
+
+
+@pytest.fixture
+def pymupdf_processor():
+    """PyMuPDF processor for testing (without image extraction)."""
+    return PyMuPDFProcessor(extract_images=False)
+
+
+async def test_pymupdf_processor_extracts_text_and_metadata(pymupdf_processor):
+    """Test PyMuPDF processor extracts text and metadata from PDF."""
+    pdf_bytes = create_test_pdf()
+
+    result = await pymupdf_processor.process(
+        content=pdf_bytes,
+        content_type="application/pdf",
+        filename="test-admin-guide.pdf",
+    )
+
+    # Verify result structure
+    assert result.success is True
+    assert result.processor == "pymupdf"
+    assert result.text is not None
+    assert len(result.text) > 0
+
+    # Verify extracted text contains expected content
+    assert "Nextcloud Administration Guide" in result.text
+    assert "Chapter 1: Introduction" in result.text
+    assert "Chapter 2: Installation" in result.text
+    assert "Chapter 3: Configuration" in result.text
+    assert "PHP 8.0 or higher" in result.text
+    assert "MySQL" in result.text
+
+    # Verify metadata
+    assert result.metadata is not None
+    assert result.metadata["page_count"] == 3
+    assert result.metadata["filename"] == "test-admin-guide.pdf"
+    assert "format" in result.metadata
+
+
+async def test_document_chunker_preserves_page_numbers():
+    """Test that document chunker can handle chunks with page number metadata."""
+    # Create chunks with page numbers
+    chunks = [
+        ChunkWithPosition(
+            text="Chapter 1 content on page 1",
+            start_offset=0,
+            end_offset=28,
+            page_number=1,
+        ),
+        ChunkWithPosition(
+            text="Chapter 2 content on page 2",
+            start_offset=29,
+            end_offset=57,
+            page_number=2,
+        ),
+        ChunkWithPosition(
+            text="Chapter 3 content on page 3",
+            start_offset=58,
+            end_offset=86,
+            page_number=3,
+        ),
+    ]
+
+    # Verify page numbers are preserved
+    assert chunks[0].page_number == 1
+    assert chunks[1].page_number == 2
+    assert chunks[2].page_number == 3
+
+
+async def test_pdf_indexing_and_search_flow(
+    pymupdf_processor: PyMuPDFProcessor,
+    qdrant_test_client: AsyncQdrantClient,
+    test_collection: str,
+    simple_embedding_provider: SimpleEmbeddingProvider,
+):
+    """Test complete PDF indexing and semantic search flow."""
+
+    # Step 1: Process PDF with PyMuPDF
+    pdf_bytes = create_test_pdf()
+    result = await pymupdf_processor.process(
+        content=pdf_bytes,
+        content_type="application/pdf",
+        filename="/Documents/admin-guide.pdf",
+    )
+
+    assert result.success is True
+    assert result.metadata["page_count"] == 3
+
+    # Step 2: Chunk the extracted text
+    # Note: In real implementation, we'd track which chunk came from which page
+    # For this test, we'll simulate by creating chunks manually
+    splitter = RecursiveCharacterTextSplitter(chunk_size=500, chunk_overlap=50)
+    chunks = splitter.split_text(result.text)
+
+    assert len(chunks) > 0
+
+    # Step 3: Index chunks into Qdrant with PDF metadata
+    points = []
+    for idx, chunk_text in enumerate(chunks):
+        embedding = await simple_embedding_provider.embed(chunk_text)
+
+        # Simulate page number assignment (in real implementation, this would be tracked)
+        # For simplicity, assign page based on content
+        page_number = 1
+        if "Chapter 2" in chunk_text or "Installation" in chunk_text:
+            page_number = 2
+        elif "Chapter 3" in chunk_text or "Configuration" in chunk_text:
+            page_number = 3
+
+        points.append(
+            PointStruct(
+                id=idx,
+                vector=embedding,
+                payload={
+                    "user_id": "admin",
+                    "doc_id": "/Documents/admin-guide.pdf",
+                    "doc_type": "file",
+                    "title": "Nextcloud Administration Guide",
+                    "file_path": "/Documents/admin-guide.pdf",
+                    "mime_type": "application/pdf",
+                    "page_number": page_number,
+                    "page_count": result.metadata["page_count"],
+                    "chunk_index": idx,
+                    "excerpt": chunk_text[:200],
+                },
+            )
+        )
+
+    await qdrant_test_client.upsert(
+        collection_name=test_collection, points=points, wait=True
+    )
+
+    # Step 4: Perform semantic search for installation instructions
+    query = "how to install Nextcloud system requirements"
+    query_embedding = await simple_embedding_provider.embed(query)
+
+    response = await qdrant_test_client.query_points(
+        collection_name=test_collection,
+        query=query_embedding,
+        limit=3,
+        score_threshold=0.0,
+    )
+
+    # Verify search results
+    assert len(response.points) > 0
+
+    # Top result should be from installation chapter (page 2)
+    top_result = response.points[0]
+    assert top_result.payload["doc_type"] == "file"
+    assert top_result.payload["file_path"] == "/Documents/admin-guide.pdf"
+    assert (
+        "Installation" in top_result.payload["excerpt"]
+        or top_result.payload["page_number"] == 2
+    )
+
+    # Verify page number is preserved
+    assert top_result.payload["page_number"] in [1, 2, 3]
+    assert top_result.payload["page_count"] == 3
+
+    # Step 5: Search for configuration
+    query = "database configuration settings MySQL"
+    query_embedding = await simple_embedding_provider.embed(query)
+
+    response = await qdrant_test_client.query_points(
+        collection_name=test_collection,
+        query=query_embedding,
+        limit=3,
+        score_threshold=0.0,
+    )
+
+    assert len(response.points) > 0
+
+    # Should find configuration chapter (page 3)
+    found_config = any(
+        "Configuration" in r.payload["excerpt"] or r.payload["page_number"] == 3
+        for r in response.points[:2]
+    )
+    assert found_config
+
+
+async def test_pdf_search_with_filters(
+    pymupdf_processor: PyMuPDFProcessor,
+    qdrant_test_client: AsyncQdrantClient,
+    test_collection: str,
+    simple_embedding_provider: SimpleEmbeddingProvider,
+):
+    """Test PDF search with metadata filters."""
+    from qdrant_client.models import FieldCondition, Filter, MatchValue
+
+    # Process and index PDF
+    pdf_bytes = create_test_pdf()
+    result = await pymupdf_processor.process(
+        content=pdf_bytes,
+        content_type="application/pdf",
+        filename="/Documents/admin-guide.pdf",
+    )
+
+    splitter = RecursiveCharacterTextSplitter(chunk_size=500, chunk_overlap=50)
+    chunks = splitter.split_text(result.text)
+
+    # Index with metadata
+    points = []
+    for idx, chunk_text in enumerate(chunks):
+        embedding = await simple_embedding_provider.embed(chunk_text)
+
+        points.append(
+            PointStruct(
+                id=idx,
+                vector=embedding,
+                payload={
+                    "user_id": "admin",
+                    "doc_id": "/Documents/admin-guide.pdf",
+                    "doc_type": "file",
+                    "mime_type": "application/pdf",
+                    "excerpt": chunk_text[:200],
+                },
+            )
+        )
+
+    await qdrant_test_client.upsert(
+        collection_name=test_collection, points=points, wait=True
+    )
+
+    # Search with filter for PDFs only
+    query = "Nextcloud installation"
+    query_embedding = await simple_embedding_provider.embed(query)
+
+    response = await qdrant_test_client.query_points(
+        collection_name=test_collection,
+        query=query_embedding,
+        query_filter=Filter(
+            must=[FieldCondition(key="doc_type", match=MatchValue(value="file"))]
+        ),
+        limit=3,
+    )
+
+    # All results should be from file documents
+    assert len(response.points) > 0
+    for result in response.points:
+        assert result.payload["doc_type"] == "file"
+        assert result.payload["mime_type"] == "application/pdf"
+
+
+async def test_pymupdf_health_check(pymupdf_processor: PyMuPDFProcessor):
+    """Test PyMuPDF processor health check."""
+    is_healthy = await pymupdf_processor.health_check()
+    assert is_healthy is True
+
+
+async def test_pymupdf_supports_pdf_mime_type(pymupdf_processor: PyMuPDFProcessor):
+    """Test PyMuPDF processor declares PDF support."""
+    assert "application/pdf" in pymupdf_processor.supported_mime_types
+    assert pymupdf_processor.name == "pymupdf"

tests/unit/client/test_webdav.py

@@ -0,0 +1,119 @@
+"""Unit tests for WebDAV client."""
+
+from unittest.mock import AsyncMock
+
+import pytest
+
+from nextcloud_mcp_server.client.webdav import WebDAVClient
+
+
+@pytest.mark.unit
+async def test_find_by_tag_calls_search_files(mocker):
+    """Test that find_by_tag constructs correct search query."""
+    # Create mock HTTP client
+    mock_http_client = AsyncMock()
+
+    # Create WebDAVClient instance
+    client = WebDAVClient(mock_http_client, "testuser")
+
+    # Mock the search_files method to avoid actual HTTP calls
+    mock_search_files = mocker.patch.object(client, "search_files", return_value=[])
+
+    # Call find_by_tag
+    await client.find_by_tag("vector-index")
+
+    # Verify search_files was called with correct parameters
+    mock_search_files.assert_called_once()
+    call_args = mock_search_files.call_args
+
+    # Check that the where_conditions contains the tag name
+    assert "vector-index" in call_args.kwargs["where_conditions"]
+    assert "<oc:tags/>" in call_args.kwargs["where_conditions"]
+    assert "<d:like>" in call_args.kwargs["where_conditions"]
+
+    # Check that tags property is requested
+    assert "tags" in call_args.kwargs["properties"]
+
+
+@pytest.mark.unit
+async def test_find_by_tag_with_scope_and_limit(mocker):
+    """Test find_by_tag passes scope and limit parameters."""
+    mock_http_client = AsyncMock()
+    client = WebDAVClient(mock_http_client, "testuser")
+
+    mock_search_files = mocker.patch.object(client, "search_files", return_value=[])
+
+    # Call with scope and limit
+    await client.find_by_tag("test-tag", scope="Documents", limit=10)
+
+    # Verify parameters were passed through
+    call_args = mock_search_files.call_args
+    assert call_args.kwargs["scope"] == "Documents"
+    assert call_args.kwargs["limit"] == 10
+
+
+@pytest.mark.unit
+def test_parse_search_response_with_tags(mocker):
+    """Test that _parse_search_response correctly parses tags."""
+    mock_http_client = AsyncMock()
+    client = WebDAVClient(mock_http_client, "testuser")
+
+    # Mock XML response with tags (comma-separated format)
+    xml_content = b"""<?xml version="1.0"?>
+    <d:multistatus xmlns:d="DAV:" xmlns:oc="http://owncloud.org/ns">
+        <d:response>
+            <d:href>/remote.php/dav/files/testuser/Documents/test.pdf</d:href>
+            <d:propstat>
+                <d:prop>
+                    <d:displayname>test.pdf</d:displayname>
+                    <d:getcontenttype>application/pdf</d:getcontenttype>
+                    <d:getcontentlength>1024</d:getcontentlength>
+                    <d:getetag>"abc123"</d:getetag>
+                    <oc:fileid>12345</oc:fileid>
+                    <oc:tags>vector-index,important</oc:tags>
+                    <d:resourcetype/>
+                </d:prop>
+            </d:propstat>
+        </d:response>
+    </d:multistatus>"""
+
+    # Parse the response
+    results = client._parse_search_response(xml_content, scope="Documents")
+
+    # Verify tags were parsed correctly
+    assert len(results) == 1
+    assert "tags" in results[0]
+    assert results[0]["tags"] == ["vector-index", "important"]
+    assert results[0]["name"] == "test.pdf"
+    assert results[0]["content_type"] == "application/pdf"
+
+
+@pytest.mark.unit
+def test_parse_search_response_with_empty_tags(mocker):
+    """Test that _parse_search_response handles files without tags."""
+    mock_http_client = AsyncMock()
+    client = WebDAVClient(mock_http_client, "testuser")
+
+    # Mock XML response without tags
+    xml_content = b"""<?xml version="1.0"?>
+    <d:multistatus xmlns:d="DAV:" xmlns:oc="http://owncloud.org/ns">
+        <d:response>
+            <d:href>/remote.php/dav/files/testuser/Documents/test.txt</d:href>
+            <d:propstat>
+                <d:prop>
+                    <d:displayname>test.txt</d:displayname>
+                    <d:getcontenttype>text/plain</d:getcontenttype>
+                    <oc:tags/>
+                    <d:resourcetype/>
+                </d:prop>
+            </d:propstat>
+        </d:response>
+    </d:multistatus>"""
+
+    # Parse the response
+    results = client._parse_search_response(xml_content, scope="Documents")
+
+    # Verify tags field is empty list
+    assert len(results) == 1
+    assert "tags" in results[0]
+    assert results[0]["tags"] == []

tests/unit/test_document_chunker.py

@@ -9,12 +9,12 @@ from nextcloud_mcp_server.vector.document_chunker import (
 class TestDocumentChunkerPositions:
     """Test suite for DocumentChunker position tracking functionality."""
 
-    def test_single_chunk_simple_text(self):
+    async def test_single_chunk_simple_text(self):
         """Test that single-chunk documents return correct positions."""
         chunker = DocumentChunker(chunk_size=2048, overlap=200)
         content = "This is a short document."
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         assert len(chunks) == 1
         assert isinstance(chunks[0], ChunkWithPosition)
@@ -22,7 +22,7 @@ class TestDocumentChunkerPositions:
         assert chunks[0].start_offset == 0
         assert chunks[0].end_offset == len(content)
 
-    def test_multiple_chunks_positions(self):
+    async def test_multiple_chunks_positions(self):
         """Test that multi-chunk documents have correct positions."""
         # Use small chunk size to force multiple chunks
         chunker = DocumentChunker(chunk_size=50, overlap=10)
@@ -34,7 +34,7 @@ class TestDocumentChunkerPositions:
             "This is the fourth sentence adding more context."
         )
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Verify we got multiple chunks
         assert len(chunks) > 1
@@ -61,12 +61,12 @@ class TestDocumentChunkerPositions:
             extracted = content[chunk.start_offset : chunk.end_offset]
             assert extracted == chunk.text
 
-    def test_chunk_positions_with_whitespace(self):
+    async def test_chunk_positions_with_whitespace(self):
         """Test position tracking with various whitespace."""
         chunker = DocumentChunker(chunk_size=30, overlap=5)
         content = "First sentence here.  Second sentence.\n\nThird sentence.\tFourth sentence."
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Verify positions correctly handle whitespace
         for chunk in chunks:
@@ -75,19 +75,19 @@ class TestDocumentChunkerPositions:
             # LangChain strips whitespace by default
             assert len(chunk.text.strip()) > 0
 
-    def test_empty_content(self):
+    async def test_empty_content(self):
         """Test that empty content returns empty chunk."""
         chunker = DocumentChunker(chunk_size=2048, overlap=200)
         content = ""
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         assert len(chunks) == 1
         assert chunks[0].text == ""
         assert chunks[0].start_offset == 0
         assert chunks[0].end_offset == 0
 
-    def test_chunk_overlap_positions(self):
+    async def test_chunk_overlap_positions(self):
         """Test that overlapping chunks have correct positions."""
         chunker = DocumentChunker(chunk_size=50, overlap=15)
         content = (
@@ -97,7 +97,7 @@ class TestDocumentChunkerPositions:
             "This is sentence four adding details."
         )
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Verify overlap exists if we have multiple chunks
         if len(chunks) > 1:
@@ -112,14 +112,14 @@ class TestDocumentChunkerPositions:
                 # With overlap, next chunk may start before current ends
                 assert next_chunk.start_offset <= current_chunk.end_offset
 
-    def test_unicode_content_positions(self):
+    async def test_unicode_content_positions(self):
         """Test position tracking with Unicode characters."""
         chunker = DocumentChunker(chunk_size=50, overlap=10)
         content = (
             "Hello 世界. こんにちは there. мир Привет world. שלום مرحبا 你好 friend."
         )
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Verify all chunks extract correctly
         for chunk in chunks:
@@ -131,7 +131,7 @@ class TestDocumentChunkerPositions:
             assert chunks[0].start_offset == 0
             assert chunks[0].end_offset == len(content)
 
-    def test_realistic_note_content(self):
+    async def test_realistic_note_content(self):
         """Test with realistic note content similar to Nextcloud Notes."""
         chunker = DocumentChunker(chunk_size=200, overlap=50)
         content = """My Project Notes
@@ -152,7 +152,7 @@ position tracking for each chunk.
 This allows us to highlight the exact chunk that matched a search query,
 which builds trust in the RAG system."""
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Should have multiple chunks
         assert len(chunks) > 1
@@ -168,7 +168,7 @@ which builds trust in the RAG system."""
             assert chunk.end_offset <= len(content)
             assert chunk.start_offset < chunk.end_offset
 
-    def test_semantic_boundary_preservation(self):
+    async def test_semantic_boundary_preservation(self):
         """Test that LangChain creates semantically coherent chunks."""
         chunker = DocumentChunker(chunk_size=100, overlap=20)
         content = (
@@ -178,7 +178,7 @@ which builds trust in the RAG system."""
             "Fourth sentence ends."
         )
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Verify all chunks are extractable using their positions
         for chunk in chunks:
@@ -193,7 +193,7 @@ which builds trust in the RAG system."""
             assert chunk.end_offset <= len(content)
             assert chunk.start_offset < chunk.end_offset
 
-    def test_paragraph_boundary_preservation(self):
+    async def test_paragraph_boundary_preservation(self):
         """Test that LangChain preserves paragraph boundaries."""
         chunker = DocumentChunker(chunk_size=80, overlap=15)
         content = """First paragraph here.
@@ -204,7 +204,7 @@ Third paragraph here.
 
 Fourth paragraph here."""
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # LangChain should prefer splitting at paragraph boundaries (\n\n)
         # Verify we got multiple chunks
@@ -215,7 +215,7 @@ Fourth paragraph here."""
             extracted = content[chunk.start_offset : chunk.end_offset]
             assert extracted == chunk.text
 
-    def test_default_parameters(self):
+    async def test_default_parameters(self):
         """Test that default parameters work correctly."""
         chunker = DocumentChunker()  # Use defaults: 2048 chars, 200 overlap
 
@@ -224,14 +224,14 @@ Fourth paragraph here."""
             "This is a short note with a few sentences. It should fit in one chunk."
         )
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         assert len(chunks) == 1
         assert chunks[0].text == content
         assert chunks[0].start_offset == 0
         assert chunks[0].end_offset == len(content)
 
-    def test_large_document_chunking(self):
+    async def test_large_document_chunking(self):
         """Test chunking of a large document."""
         chunker = DocumentChunker(chunk_size=100, overlap=20)
 
@@ -244,7 +244,7 @@ Fourth paragraph here."""
         ]
         content = "\n\n".join(paragraphs)
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         # Should create multiple chunks
         assert len(chunks) > 1
@@ -261,12 +261,12 @@ Fourth paragraph here."""
         assert chunks[0].start_offset == 0
         assert chunks[-1].end_offset == len(content)
 
-    def test_position_tracking_with_overlap(self):
+    async def test_position_tracking_with_overlap(self):
         """Test that position tracking works correctly with overlap."""
         chunker = DocumentChunker(chunk_size=50, overlap=15)
         content = "A" * 25 + ". " + "B" * 25 + ". " + "C" * 25 + ". " + "D" * 25 + "."
 
-        chunks = chunker.chunk_text(content)
+        chunks = await chunker.chunk_text(content)
 
         if len(chunks) > 1:
             # Verify overlap creates correct positions

tools/parse-doc.py

@@ -0,0 +1,41 @@
+import logging
+import pathlib
+
+import anyio
+import pymupdf
+import pymupdf.layout
+
+from nextcloud_mcp_server.client import NextcloudClient
+
+pymupdf.layout.activate()
+import pymupdf4llm  # noqa: E402
+
+client = NextcloudClient.from_env()
+logger = logging.getLogger(__name__)
+
+TMP_DIR = pathlib.Path("/tmp/tmp-images")
+TMP_DIR.mkdir(exist_ok=True, parents=True)
+
+
+async def print_markdown(filename):
+    content, _ = await client.webdav.read_file(filename)
+    doc = pymupdf.open("pdf", content)
+    md_text = pymupdf4llm.to_markdown(doc, write_images=True, image_path=str(TMP_DIR))
+    print(md_text)
+
+
+async def run1():
+    response = await client.webdav.find_by_type("application/pdf")
+    # print(response)
+    for file in response:
+        await print_markdown(file["path"])
+
+
+async def run():
+    tags = await client.tags.get_all_tags()
+    print(tags)
+
+
+if __name__ == "__main__":
+    logging.basicConfig(level="INFO")
+    anyio.run(run)

uv.lock

@@ -1645,7 +1645,7 @@ wheels = [
 
 [[package]]
 name = "mcp"
-version = "1.21.1"
+version = "1.22.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
@@ -1663,9 +1663,9 @@ dependencies = [
     { name = "typing-inspection" },
     { name = "uvicorn", marker = "sys_platform != 'emscripten'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/f7/25/4df633e7574254ada574822db2245bbee424725d1b01bccae10bf128794e/mcp-1.21.1.tar.gz", hash = "sha256:540e6ac4b12b085c43f14879fde04cbdb10148a09ea9492ff82d8c7ba651a302", size = 469071, upload-time = "2025-11-13T20:33:46.139Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/a3/a2/c5ec0ab38b35ade2ae49a90fada718fbc76811dc5aa1760414c6aaa6b08a/mcp-1.22.0.tar.gz", hash = "sha256:769b9ac90ed42134375b19e777a2858ca300f95f2e800982b3e2be62dfc0ba01", size = 471788, upload-time = "2025-11-20T20:11:28.095Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/49/af/01fb42df59ad15925ffc1e2e609adafddd3ac4572f606faae0dc8b55ba0c/mcp-1.21.1-py3-none-any.whl", hash = "sha256:dd35abe36d68530a8a1291daa25d50276d8731e545c0434d6e250a3700dd2a6d", size = 174852, upload-time = "2025-11-13T20:33:44.502Z" },
+    { url = "https://files.pythonhosted.org/packages/a9/bb/711099f9c6bb52770f56e56401cdfb10da5b67029f701e0df29362df4c8e/mcp-1.22.0-py3-none-any.whl", hash = "sha256:bed758e24df1ed6846989c909ba4e3df339a27b4f30f1b8b627862a4bade4e98", size = 175489, upload-time = "2025-11-20T20:11:26.542Z" },
 ]
 
 [package.optional-dependencies]
@@ -1925,9 +1925,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/6c/28/dd72947e59a6a8c856448a5e74da6201cb5502ddff644fbc790e4bd40b9a/multiprocess-0.70.18-py39-none-any.whl", hash = "sha256:e78ca805a72b1b810c690b6b4cc32579eba34f403094bbbae962b7b5bf9dfcb8", size = 133478, upload-time = "2025-04-17T03:11:26.253Z" },
 ]
 
+[[package]]
+name = "networkx"
+version = "3.5"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/6c/4f/ccdb8ad3a38e583f214547fd2f7ff1fc160c43a75af88e6aec213404b96a/networkx-3.5.tar.gz", hash = "sha256:d4c6f9cf81f52d69230866796b82afbccdec3db7ae4fbd1b65ea750feed50037", size = 2471065, upload-time = "2025-05-29T11:35:07.804Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/eb/8d/776adee7bbf76365fdd7f2552710282c79a4ead5d2a46408c9043a2b70ba/networkx-3.5-py3-none-any.whl", hash = "sha256:0030d386a9a06dee3565298b4a734b68589749a544acbb6c412dc9e2489ec6ec", size = 2034406, upload-time = "2025-05-29T11:35:04.961Z" },
+]
+
 [[package]]
 name = "nextcloud-mcp-server"
-version = "0.44.0"
+version = "0.46.2"
 source = { editable = "." }
 dependencies = [
     { name = "aiosqlite" },
@@ -1952,6 +1961,9 @@ dependencies = [
     { name = "prometheus-client" },
     { name = "pydantic" },
     { name = "pyjwt", extra = ["crypto"] },
+    { name = "pymupdf" },
+    { name = "pymupdf-layout" },
+    { name = "pymupdf4llm" },
     { name = "python-json-logger" },
     { name = "pythonvcard4" },
     { name = "qdrant-client" },
@@ -1986,7 +1998,7 @@ requires-dist = [
     { name = "icalendar", specifier = ">=6.0.0,<7.0.0" },
     { name = "jinja2", specifier = ">=3.1.6" },
     { name = "langchain-text-splitters", specifier = ">=1.0.0" },
-    { name = "mcp", extras = ["cli"], specifier = ">=1.21,<1.22" },
+    { name = "mcp", extras = ["cli"], specifier = ">=1.22,<1.23" },
     { name = "opentelemetry-api", specifier = ">=1.28.2" },
     { name = "opentelemetry-exporter-otlp-proto-grpc", specifier = ">=1.28.2" },
     { name = "opentelemetry-instrumentation-asgi", specifier = ">=0.49b2" },
@@ -1997,6 +2009,9 @@ requires-dist = [
     { name = "prometheus-client", specifier = ">=0.21.0" },
     { name = "pydantic", specifier = ">=2.11.4" },
     { name = "pyjwt", extras = ["crypto"], specifier = ">=2.8.0" },
+    { name = "pymupdf", specifier = ">=1.26.6" },
+    { name = "pymupdf-layout", specifier = ">=1.26.6" },
+    { name = "pymupdf4llm", specifier = ">=0.2.2" },
     { name = "python-json-logger", specifier = ">=3.2.0" },
     { name = "pythonvcard4", specifier = ">=0.2.0" },
     { name = "qdrant-client", specifier = ">=1.7.0" },
@@ -2969,6 +2984,52 @@ crypto = [
     { name = "cryptography" },
 ]
 
+[[package]]
+name = "pymupdf"
+version = "1.26.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/ec/d7/a6f0e03a117fa2ad79c4b898203bb212b17804f92558a6a339298faca7bb/pymupdf-1.26.6.tar.gz", hash = "sha256:a2b4531cd4ab36d6f1f794bb6d3c33b49bda22f36d58bb1f3e81cbc10183bd2b", size = 84322494, upload-time = "2025-11-05T15:20:46.786Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/9e/5c/dec354eee5fe4966c715f33818ed4193e0e6c986cf8484de35b6c167fb8e/pymupdf-1.26.6-cp310-abi3-macosx_10_9_x86_64.whl", hash = "sha256:e46f320a136ad55e5219e8f0f4061bdf3e4c12b126d2740d5a49f73fae7ea176", size = 23178988, upload-time = "2025-11-05T14:31:19.834Z" },
+    { url = "https://files.pythonhosted.org/packages/ec/a0/11adb742d18142bd623556cd3b5d64649816decc5eafd30efc9498657e76/pymupdf-1.26.6-cp310-abi3-macosx_11_0_arm64.whl", hash = "sha256:6844cd2396553c0fa06de4869d5d5ecb1260e6fc3b9d85abe8fa35f14dd9d688", size = 22469764, upload-time = "2025-11-05T14:32:34.654Z" },
+    { url = "https://files.pythonhosted.org/packages/e4/c8/377cf20e31f58d4c243bfcf2d3cb7466d5b97003b10b9f1161f11eb4a994/pymupdf-1.26.6-cp310-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:617ba69e02c44f0da1c0e039ea4a26cf630849fd570e169c71daeb8ac52a81d6", size = 23502227, upload-time = "2025-11-06T11:03:56.934Z" },
+    { url = "https://files.pythonhosted.org/packages/4f/bf/6e02e3d84b32c137c71a0a3dcdba8f2f6e9950619a3bc272245c7c06a051/pymupdf-1.26.6-cp310-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:7777d0b7124c2ebc94849536b6a1fb85d158df3b9d873935e63036559391534c", size = 24115381, upload-time = "2025-11-05T14:33:54.338Z" },
+    { url = "https://files.pythonhosted.org/packages/ab/9d/30f7fcb3776bfedde66c06297960debe4883b1667294a1ee9426c942e94d/pymupdf-1.26.6-cp310-abi3-win32.whl", hash = "sha256:8f3ef05befc90ca6bb0f12983200a7048d5bff3e1c1edef1bb3de60b32cb5274", size = 17203613, upload-time = "2025-11-05T17:19:47.494Z" },
+    { url = "https://files.pythonhosted.org/packages/f9/e8/989f4eaa369c7166dc24f0eaa3023f13788c40ff1b96701f7047421554a8/pymupdf-1.26.6-cp310-abi3-win_amd64.whl", hash = "sha256:ce02ca96ed0d1acfd00331a4d41a34c98584d034155b06fd4ec0f051718de7ba", size = 18405680, upload-time = "2025-11-05T14:34:48.672Z" },
+]
+
+[[package]]
+name = "pymupdf-layout"
+version = "1.26.6"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "networkx" },
+    { name = "numpy" },
+    { name = "onnxruntime" },
+    { name = "pymupdf" },
+    { name = "pyyaml" },
+]
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