bump: version 0.31.0 → 0.31.1

refactor: simplify OpenTelemetry tracing configuration

.gitignore

@@ -5,5 +5,7 @@ __pycache__/
 .env.local
 .env.*.local
 
+docker-compose.override.yml
+
 # Generated by pytest used to login users
 .nextcloud_oauth_*.json

CHANGELOG.md

@@ -1,3 +1,9 @@
+## v0.31.1 (2025-11-10)
+
+### Refactor
+
+- simplify OpenTelemetry tracing configuration
+
 ## v0.31.0 (2025-11-10)
 
 ### Feat

Dockerfile

@@ -9,7 +9,7 @@ WORKDIR /app
 
 COPY . .
 
-RUN uv sync --locked --no-dev
+RUN uv sync --locked --no-dev --no-editable
 
 ENV PYTHONUNBUFFERED=1
 ENV VIRTUAL_ENV=/app/.venv

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: 0.31.0
-appVersion: "0.31.0"
+version: 0.31.1
+appVersion: "0.31.1"
 keywords:
   - nextcloud
   - mcp

charts/nextcloud-mcp-server/templates/deployment.yaml

@@ -218,8 +218,6 @@ spec:
             - name: METRICS_PORT
               value: {{ .Values.observability.metrics.port | quote }}
             {{- if .Values.observability.tracing.enabled }}
-            - name: OTEL_ENABLED
-              value: "true"
             - name: OTEL_EXPORTER_OTLP_ENDPOINT
               value: {{ .Values.observability.tracing.endpoint | quote }}
             - name: OTEL_SERVICE_NAME

docker-compose.yml

@@ -98,16 +98,20 @@ services:
       #- QDRANT_URL=http://qdrant:6333  # Uncomment for network mode
       #- QDRANT_API_KEY=${QDRANT_API_KEY:-my_secret_api_key}  # Only for network mode
 
+      # Observability
+      #- OTEL_SERVICE_NAME=nextcloud-mcp-docker-compose
+      #- OTEL_EXPORTER_OTLP_ENDPOINT=http://otel-collector:4317
+
       # Collection naming: Auto-generated as {deployment-id}-{model-name}
       # - Deployment ID: OTEL_SERVICE_NAME (if set) or hostname (fallback)
       # - Model name: OLLAMA_EMBEDDING_MODEL
       # - Example: "nextcloud-mcp-server-nomic-embed-text"
       # - Changing models creates new collection (requires re-embedding)
       # - Set QDRANT_COLLECTION to override auto-generation:
-      - QDRANT_COLLECTION=nextcloud_content
+      #- QDRANT_COLLECTION=nextcloud_content
 
       # Ollama configuration (optional - uses SimpleEmbeddingProvider if not set)
-      # - OLLAMA_BASE_URL=https://ollama.internal.coutinho.io:443
+      # - OLLAMA_BASE_URL=http://ollama:11434
       # - OLLAMA_EMBEDDING_MODEL=nomic-embed-text  # Changing this creates new collection
       # - OLLAMA_VERIFY_SSL=false
 

docs/observability.md

@@ -16,8 +16,7 @@ The Nextcloud MCP Server includes comprehensive observability features for produ
 export METRICS_ENABLED=true
 export METRICS_PORT=9090
 
-# Enable tracing (optional)
-export OTEL_ENABLED=true
+# Enable tracing (optional - tracing is enabled when OTEL_EXPORTER_OTLP_ENDPOINT is set)
 export OTEL_EXPORTER_OTLP_ENDPOINT=http://localhost:4317
 
 # Start the server
@@ -46,8 +45,7 @@ helm install nextcloud-mcp charts/nextcloud-mcp-server \
 |----------|---------|-------------|
 | `METRICS_ENABLED` | `true` | Enable Prometheus metrics |
 | `METRICS_PORT` | `9090` | Port for metrics endpoint |
-| `OTEL_ENABLED` | `false` | Enable OpenTelemetry tracing |
-| `OTEL_EXPORTER_OTLP_ENDPOINT` | - | OTLP gRPC endpoint (e.g., `http://otel-collector:4317`) |
+| `OTEL_EXPORTER_OTLP_ENDPOINT` | - | OTLP gRPC endpoint (e.g., `http://otel-collector:4317`). Tracing is enabled when this is set. |
 | `OTEL_SERVICE_NAME` | `nextcloud-mcp-server` | Service name in traces |
 | `OTEL_TRACES_SAMPLER` | `always_on` | Trace sampling strategy |
 | `OTEL_TRACES_SAMPLER_ARG` | `1.0` | Sampling rate (0.0-1.0) |

nextcloud_mcp_server/app.py

@@ -5,9 +5,12 @@ from contextlib import AsyncExitStack, asynccontextmanager
 from dataclasses import dataclass
 from typing import TYPE_CHECKING, Optional
 
+from opentelemetry.instrumentation.httpx import HTTPXClientInstrumentor
+
 if TYPE_CHECKING:
     from nextcloud_mcp_server.auth.refresh_token_storage import RefreshTokenStorage
 
+
 import anyio
 import click
 import httpx
@@ -58,6 +61,7 @@ from nextcloud_mcp_server.server.oauth_tools import register_oauth_tools
 from nextcloud_mcp_server.vector import processor_task, scanner_task
 
 logger = logging.getLogger(__name__)
+HTTPXClientInstrumentor().instrument()
 
 
 def initialize_document_processors():
@@ -791,17 +795,20 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
         )
 
     # Setup OpenTelemetry tracing (optional)
-    if settings.tracing_enabled:
+    if settings.otel_exporter_otlp_endpoint:
         setup_tracing(
             service_name=settings.otel_service_name,
             otlp_endpoint=settings.otel_exporter_otlp_endpoint,
+            otlp_verify_ssl=settings.otel_exporter_verify_ssl,
             sampling_rate=settings.otel_traces_sampler_arg,
         )
         logger.info(
             f"OpenTelemetry tracing enabled (endpoint: {settings.otel_exporter_otlp_endpoint})"
         )
     else:
-        logger.info("OpenTelemetry tracing disabled (set OTEL_ENABLED=true to enable)")
+        logger.info(
+            "OpenTelemetry tracing disabled (set OTEL_EXPORTER_OTLP_ENDPOINT to enable)"
+        )
 
     # Determine authentication mode
     oauth_enabled = is_oauth_mode()
@@ -1391,9 +1398,12 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
                 )
                 logger.info(f"🔑 /mcp request with Authorization: {token_preview}")
             else:
-                logger.warning(
-                    f"⚠️  /mcp request WITHOUT Authorization header from {request.client}"
-                )
+                # Only warn about missing Authorization in OAuth mode
+                # In BasicAuth mode, /mcp requests without Authorization are expected
+                if oauth_enabled:
+                    logger.warning(
+                        f"⚠️  /mcp request WITHOUT Authorization header from {request.client}"
+                    )
 
             # Log client capabilities on initialize request
             if request.method == "POST":
@@ -1454,7 +1464,7 @@ def get_app(transport: str = "sse", enabled_apps: list[str] | None = None):
     )
 
     # Add observability middleware (metrics + tracing)
-    if settings.metrics_enabled or settings.tracing_enabled:
+    if settings.metrics_enabled or settings.otel_exporter_otlp_endpoint:
         app.add_middleware(ObservabilityMiddleware)
         logger.info("Observability middleware enabled (metrics and/or tracing)")
 

nextcloud_mcp_server/auth/unified_verifier.py

@@ -231,17 +231,21 @@ class UnifiedTokenVerifier(TokenVerifier):
                 token,
                 signing_key.key,
                 algorithms=["RS256"],
-                issuer=self.settings.oidc_issuer
-                if hasattr(self.settings, "oidc_issuer")
-                else None,
+                issuer=(
+                    self.settings.oidc_issuer
+                    if hasattr(self.settings, "oidc_issuer")
+                    else None
+                ),
                 options={
                     "verify_signature": True,
                     "verify_exp": True,
                     "verify_iat": True,
-                    "verify_iss": True
-                    if hasattr(self.settings, "oidc_issuer")
-                    and self.settings.oidc_issuer
-                    else False,
+                    "verify_iss": (
+                        True
+                        if hasattr(self.settings, "oidc_issuer")
+                        and self.settings.oidc_issuer
+                        else False
+                    ),
                     "verify_aud": False,  # We handle audience validation separately
                 },
             )

nextcloud_mcp_server/client/__init__.py

@@ -9,6 +9,7 @@ from httpx import (
     BasicAuth,
     Request,
     Response,
+    Timeout,
 )
 
 from ..controllers.notes_search import NotesSearchController
@@ -66,6 +67,7 @@ class NextcloudClient:
             auth=auth,
             transport=AsyncDisableCookieTransport(AsyncHTTPTransport()),
             event_hooks={"request": [log_request], "response": [log_response]},
+            timeout=Timeout(timeout=30, connect=5),
         )
 
         # Initialize app clients

nextcloud_mcp_server/config.py

@@ -181,8 +181,8 @@ class Settings:
     # Observability settings
     metrics_enabled: bool = True
     metrics_port: int = 9090
-    tracing_enabled: bool = False
     otel_exporter_otlp_endpoint: Optional[str] = None
+    otel_exporter_verify_ssl: bool = False
     otel_service_name: str = "nextcloud-mcp-server"
     otel_traces_sampler: str = "always_on"
     otel_traces_sampler_arg: float = 1.0
@@ -334,8 +334,9 @@ def get_settings() -> Settings:
         # Observability settings
         metrics_enabled=os.getenv("METRICS_ENABLED", "true").lower() == "true",
         metrics_port=int(os.getenv("METRICS_PORT", "9090")),
-        tracing_enabled=os.getenv("OTEL_ENABLED", "false").lower() == "true",
         otel_exporter_otlp_endpoint=os.getenv("OTEL_EXPORTER_OTLP_ENDPOINT"),
+        otel_exporter_verify_ssl=os.getenv("OTEL_EXPORTER_VERIFY_SSL", "false").lower()
+        == "true",
         otel_service_name=os.getenv("OTEL_SERVICE_NAME", "nextcloud-mcp-server"),
         otel_traces_sampler=os.getenv("OTEL_TRACES_SAMPLER", "always_on"),
         otel_traces_sampler_arg=float(os.getenv("OTEL_TRACES_SAMPLER_ARG", "1.0")),

nextcloud_mcp_server/observability/tracing.py

@@ -13,9 +13,9 @@ import logging
 from contextlib import contextmanager
 from typing import Any
 
+from importlib_metadata import version
 from opentelemetry import trace
 from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter
-from opentelemetry.instrumentation.httpx import HTTPXClientInstrumentor
 from opentelemetry.instrumentation.logging import LoggingInstrumentor
 from opentelemetry.sdk.resources import Resource
 from opentelemetry.sdk.trace import TracerProvider
@@ -27,10 +27,13 @@ logger = logging.getLogger(__name__)
 # Global tracer instance (initialized in setup_tracing)
 _tracer: Tracer | None = None
 
+# Auto-instrument httpx for Nextcloud API calls
+
 
 def setup_tracing(
     service_name: str = "nextcloud-mcp-server",
     otlp_endpoint: str | None = None,
+    otlp_verify_ssl: bool = False,
     sampling_rate: float = 1.0,
 ) -> Tracer:
     """
@@ -40,6 +43,8 @@ def setup_tracing(
         service_name: Service name for traces (default: "nextcloud-mcp-server")
         otlp_endpoint: OTLP gRPC endpoint (e.g., "http://otel-collector:4317")
                       If None, tracing is initialized but no exporter is configured
+        otlp_verify_ssl: Enable TLS verification for otlp_endpoint. If True,
+                      `insecure` will eval to False
         sampling_rate: Sampling rate (0.0-1.0). Default 1.0 (100% sampling)
 
     Returns:
@@ -51,7 +56,7 @@ def setup_tracing(
     resource = Resource.create(
         {
             "service.name": service_name,
-            "service.version": "0.27.2",  # TODO: Extract from pyproject.toml
+            "service.version": version(__package__.split(".")[0]),
         }
     )
 
@@ -61,7 +66,9 @@ def setup_tracing(
     # Configure OTLP exporter if endpoint is provided
     if otlp_endpoint:
         try:
-            otlp_exporter = OTLPSpanExporter(endpoint=otlp_endpoint, insecure=True)
+            otlp_exporter = OTLPSpanExporter(
+                endpoint=otlp_endpoint, insecure=not otlp_verify_ssl
+            )
             span_processor = BatchSpanProcessor(otlp_exporter)
             provider.add_span_processor(span_processor)
             logger.info(
@@ -79,9 +86,6 @@ def setup_tracing(
     # Set global tracer provider
     trace.set_tracer_provider(provider)
 
-    # Auto-instrument httpx for Nextcloud API calls
-    HTTPXClientInstrumentor().instrument()
-
     # Auto-instrument logging to inject trace context
     LoggingInstrumentor().instrument(set_logging_format=True)
 

nextcloud_mcp_server/vector/processor.py

@@ -15,6 +15,7 @@ from qdrant_client.models import FieldCondition, Filter, MatchValue, PointStruct
 from nextcloud_mcp_server.client import NextcloudClient
 from nextcloud_mcp_server.config import get_settings
 from nextcloud_mcp_server.embedding import get_embedding_service
+from nextcloud_mcp_server.observability.tracing import trace_operation
 from nextcloud_mcp_server.vector.document_chunker import DocumentChunker
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 from nextcloud_mcp_server.vector.scanner import DocumentTask
@@ -94,58 +95,68 @@ async def process_document(doc_task: DocumentTask, nc_client: NextcloudClient):
         f"for {doc_task.user_id} ({doc_task.operation})"
     )
 
-    qdrant_client = await get_qdrant_client()
-    settings = get_settings()
+    with trace_operation(
+        "vector_sync.process_document",
+        attributes={
+            "vector_sync.operation": "process",
+            "vector_sync.user_id": doc_task.user_id,
+            "vector_sync.doc_id": doc_task.doc_id,
+            "vector_sync.doc_type": doc_task.doc_type,
+            "vector_sync.doc_operation": doc_task.operation,
+        },
+    ):
+        qdrant_client = await get_qdrant_client()
+        settings = get_settings()
 
-    # Handle deletion
-    if doc_task.operation == "delete":
-        await qdrant_client.delete(
-            collection_name=settings.get_collection_name(),
-            points_selector=Filter(
-                must=[
-                    FieldCondition(
-                        key="user_id",
-                        match=MatchValue(value=doc_task.user_id),
-                    ),
-                    FieldCondition(
-                        key="doc_id",
-                        match=MatchValue(value=doc_task.doc_id),
-                    ),
-                    FieldCondition(
-                        key="doc_type",
-                        match=MatchValue(value=doc_task.doc_type),
-                    ),
-                ]
-            ),
-        )
-        logger.info(
-            f"Deleted {doc_task.doc_type}_{doc_task.doc_id} for {doc_task.user_id}"
-        )
-        return
+        # Handle deletion
+        if doc_task.operation == "delete":
+            await qdrant_client.delete(
+                collection_name=settings.get_collection_name(),
+                points_selector=Filter(
+                    must=[
+                        FieldCondition(
+                            key="user_id",
+                            match=MatchValue(value=doc_task.user_id),
+                        ),
+                        FieldCondition(
+                            key="doc_id",
+                            match=MatchValue(value=doc_task.doc_id),
+                        ),
+                        FieldCondition(
+                            key="doc_type",
+                            match=MatchValue(value=doc_task.doc_type),
+                        ),
+                    ]
+                ),
+            )
+            logger.info(
+                f"Deleted {doc_task.doc_type}_{doc_task.doc_id} for {doc_task.user_id}"
+            )
+            return
 
-    # Handle indexing with retry
-    max_retries = 3
-    retry_delay = 1.0
+        # Handle indexing with retry
+        max_retries = 3
+        retry_delay = 1.0
 
-    for attempt in range(max_retries):
-        try:
-            await _index_document(doc_task, nc_client, qdrant_client)
-            return  # Success
+        for attempt in range(max_retries):
+            try:
+                await _index_document(doc_task, nc_client, qdrant_client)
+                return  # Success
 
-        except (HTTPStatusError, Exception) as e:
-            if attempt < max_retries - 1:
-                logger.warning(
-                    f"Retry {attempt + 1}/{max_retries} for "
-                    f"{doc_task.doc_type}_{doc_task.doc_id}: {e}"
-                )
-                await anyio.sleep(retry_delay)
-                retry_delay *= 2  # Exponential backoff
-            else:
-                logger.error(
-                    f"Failed to index {doc_task.doc_type}_{doc_task.doc_id} "
-                    f"after {max_retries} retries: {e}"
-                )
-                raise
+            except (HTTPStatusError, Exception) as e:
+                if attempt < max_retries - 1:
+                    logger.warning(
+                        f"Retry {attempt + 1}/{max_retries} for "
+                        f"{doc_task.doc_type}_{doc_task.doc_id}: {e}"
+                    )
+                    await anyio.sleep(retry_delay)
+                    retry_delay *= 2  # Exponential backoff
+                else:
+                    logger.error(
+                        f"Failed to index {doc_task.doc_type}_{doc_task.doc_id} "
+                        f"after {max_retries} retries: {e}"
+                    )
+                    raise
 
 
 async def _index_document(

nextcloud_mcp_server/vector/scanner.py

@@ -13,6 +13,7 @@ from qdrant_client.models import FieldCondition, Filter, MatchValue
 
 from nextcloud_mcp_server.client import NextcloudClient
 from nextcloud_mcp_server.config import get_settings
+from nextcloud_mcp_server.observability.tracing import trace_operation
 from nextcloud_mcp_server.vector.qdrant_client import get_qdrant_client
 
 logger = logging.getLogger(__name__)
@@ -154,134 +155,148 @@ async def scan_user_documents(
         f"[SCAN-{scan_id}] Starting scan for user: {user_id}, initial_sync={initial_sync}"
     )
 
-    # Calculate prune timestamp for optimized data transfer
-    # Only notes modified after this will be sent with full data
-    prune_before = None if initial_sync else await get_last_indexed_timestamp(user_id)
-    if prune_before:
-        logger.info(
-            f"[SCAN-{scan_id}] Using pruneBefore={prune_before} to optimize data transfer"
+    with trace_operation(
+        "vector_sync.scan_user_documents",
+        attributes={
+            "vector_sync.operation": "scan",
+            "vector_sync.user_id": user_id,
+            "vector_sync.initial_sync": initial_sync,
+            "vector_sync.scan_id": scan_id,
+        },
+    ):
+        # Calculate prune timestamp for optimized data transfer
+        # Only notes modified after this will be sent with full data
+        prune_before = (
+            None if initial_sync else await get_last_indexed_timestamp(user_id)
+        )
+        if prune_before:
+            logger.info(
+                f"[SCAN-{scan_id}] Using pruneBefore={prune_before} to optimize data transfer"
+            )
+
+        # Fetch all notes from Nextcloud
+        notes = [
+            note
+            async for note in nc_client.notes.get_all_notes(prune_before=prune_before)
+        ]
+        logger.info(f"[SCAN-{scan_id}] Found {len(notes)} notes for {user_id}")
+
+        if initial_sync:
+            # Send everything on first sync
+            for note in notes:
+                modified_at = note.get("modified", 0)
+                await send_stream.send(
+                    DocumentTask(
+                        user_id=user_id,
+                        doc_id=str(note["id"]),
+                        doc_type="note",
+                        operation="index",
+                        modified_at=modified_at,
+                    )
+                )
+            logger.info(f"Sent {len(notes)} documents for initial sync: {user_id}")
+            return
+
+        # Get indexed state from Qdrant
+        qdrant_client = await get_qdrant_client()
+        scroll_result = await qdrant_client.scroll(
+            collection_name=get_settings().get_collection_name(),
+            scroll_filter=Filter(
+                must=[
+                    FieldCondition(key="user_id", match=MatchValue(value=user_id)),
+                    FieldCondition(key="doc_type", match=MatchValue(value="note")),
+                ]
+            ),
+            with_payload=["doc_id", "indexed_at"],
+            with_vectors=False,
+            limit=10000,
         )
 
-    # Fetch all notes from Nextcloud
-    notes = [
-        note async for note in nc_client.notes.get_all_notes(prune_before=prune_before)
-    ]
-    logger.info(f"[SCAN-{scan_id}] Found {len(notes)} notes for {user_id}")
+        indexed_docs = {
+            point.payload["doc_id"]: point.payload["indexed_at"]
+            for point in scroll_result[0]
+        }
+
+        logger.debug(f"Found {len(indexed_docs)} indexed documents in Qdrant")
+
+        # Compare and queue changes
+        queued = 0
+        nextcloud_doc_ids = {str(note["id"]) for note in notes}
 
-    if initial_sync:
-        # Send everything on first sync
         for note in notes:
+            doc_id = str(note["id"])
+            indexed_at = indexed_docs.get(doc_id)
             modified_at = note.get("modified", 0)
-            await send_stream.send(
-                DocumentTask(
-                    user_id=user_id,
-                    doc_id=str(note["id"]),
-                    doc_type="note",
-                    operation="index",
-                    modified_at=modified_at,
-                )
-            )
-        logger.info(f"Sent {len(notes)} documents for initial sync: {user_id}")
-        return
 
-    # Get indexed state from Qdrant
-    qdrant_client = await get_qdrant_client()
-    scroll_result = await qdrant_client.scroll(
-        collection_name=get_settings().get_collection_name(),
-        scroll_filter=Filter(
-            must=[
-                FieldCondition(key="user_id", match=MatchValue(value=user_id)),
-                FieldCondition(key="doc_type", match=MatchValue(value="note")),
-            ]
-        ),
-        with_payload=["doc_id", "indexed_at"],
-        with_vectors=False,
-        limit=10000,
-    )
-
-    indexed_docs = {
-        point.payload["doc_id"]: point.payload["indexed_at"]
-        for point in scroll_result[0]
-    }
-
-    logger.debug(f"Found {len(indexed_docs)} indexed documents in Qdrant")
-
-    # Compare and queue changes
-    queued = 0
-    nextcloud_doc_ids = {str(note["id"]) for note in notes}
-
-    for note in notes:
-        doc_id = str(note["id"])
-        indexed_at = indexed_docs.get(doc_id)
-        modified_at = note.get("modified", 0)
-
-        # If document reappeared, remove from potentially_deleted
-        doc_key = (user_id, doc_id)
-        if doc_key in _potentially_deleted:
-            logger.debug(
-                f"Document {doc_id} reappeared, removing from deletion grace period"
-            )
-            del _potentially_deleted[doc_key]
-
-        # Send if never indexed or modified since last index
-        if indexed_at is None or modified_at > indexed_at:
-            await send_stream.send(
-                DocumentTask(
-                    user_id=user_id,
-                    doc_id=doc_id,
-                    doc_type="note",
-                    operation="index",
-                    modified_at=modified_at,
-                )
-            )
-            queued += 1
-
-    # Check for deleted documents (in Qdrant but not in Nextcloud)
-    # Use grace period: only delete after 2 consecutive scans confirm absence
-    settings = get_settings()
-    grace_period = settings.vector_sync_scan_interval * 1.5  # Allow 1.5 scan intervals
-    current_time = time.time()
-
-    for doc_id in indexed_docs:
-        if doc_id not in nextcloud_doc_ids:
+            # If document reappeared, remove from potentially_deleted
             doc_key = (user_id, doc_id)
-
             if doc_key in _potentially_deleted:
-                # Already marked as potentially deleted, check if grace period elapsed
-                first_missing_time = _potentially_deleted[doc_key]
-                time_missing = current_time - first_missing_time
-
-                if time_missing >= grace_period:
-                    # Grace period elapsed, send for deletion
-                    logger.info(
-                        f"Document {doc_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=doc_id,
-                            doc_type="note",
-                            operation="delete",
-                            modified_at=0,
-                        )
-                    )
-                    queued += 1
-                    # Remove from tracking after sending deletion
-                    del _potentially_deleted[doc_key]
-                else:
-                    logger.debug(
-                        f"Document {doc_id} still missing "
-                        f"({time_missing:.1f}s/{grace_period:.1f}s grace period)"
-                    )
-            else:
-                # First time missing, add to grace period tracking
                 logger.debug(
-                    f"Document {doc_id} missing for first time, starting grace period"
+                    f"Document {doc_id} reappeared, removing from deletion grace period"
                 )
-                _potentially_deleted[doc_key] = current_time
+                del _potentially_deleted[doc_key]
 
-    if queued > 0:
-        logger.info(f"Sent {queued} documents for incremental sync: {user_id}")
-    else:
-        logger.debug(f"No changes detected for {user_id}")
+            # Send if never indexed or modified since last index
+            if indexed_at is None or modified_at > indexed_at:
+                await send_stream.send(
+                    DocumentTask(
+                        user_id=user_id,
+                        doc_id=doc_id,
+                        doc_type="note",
+                        operation="index",
+                        modified_at=modified_at,
+                    )
+                )
+                queued += 1
+
+        # Check for deleted documents (in Qdrant but not in Nextcloud)
+        # Use grace period: only delete after 2 consecutive scans confirm absence
+        settings = get_settings()
+        grace_period = (
+            settings.vector_sync_scan_interval * 1.5
+        )  # Allow 1.5 scan intervals
+        current_time = time.time()
+
+        for doc_id in indexed_docs:
+            if doc_id not in nextcloud_doc_ids:
+                doc_key = (user_id, doc_id)
+
+                if doc_key in _potentially_deleted:
+                    # Already marked as potentially deleted, check if grace period elapsed
+                    first_missing_time = _potentially_deleted[doc_key]
+                    time_missing = current_time - first_missing_time
+
+                    if time_missing >= grace_period:
+                        # Grace period elapsed, send for deletion
+                        logger.info(
+                            f"Document {doc_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=doc_id,
+                                doc_type="note",
+                                operation="delete",
+                                modified_at=0,
+                            )
+                        )
+                        queued += 1
+                        # Remove from tracking after sending deletion
+                        del _potentially_deleted[doc_key]
+                    else:
+                        logger.debug(
+                            f"Document {doc_id} still missing "
+                            f"({time_missing:.1f}s/{grace_period:.1f}s grace period)"
+                        )
+                else:
+                    # First time missing, add to grace period tracking
+                    logger.debug(
+                        f"Document {doc_id} missing for first time, starting grace period"
+                    )
+                    _potentially_deleted[doc_key] = current_time
+
+        if queued > 0:
+            logger.info(f"Sent {queued} documents 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 = "0.31.0"
+version = "0.31.1"
 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"}
@@ -23,14 +23,14 @@ dependencies = [
     "authlib>=1.6.5",
     "qdrant-client>=1.7.0",
     # Observability dependencies
-    "prometheus-client>=0.21.0",  # Prometheus metrics
-    "opentelemetry-api>=1.28.2",  # OpenTelemetry API
-    "opentelemetry-sdk>=1.28.2",  # OpenTelemetry SDK
-    "opentelemetry-instrumentation-asgi>=0.49b2",  # Auto-instrument ASGI/Starlette
-    "opentelemetry-instrumentation-httpx>=0.49b2",  # Auto-instrument httpx client
-    "opentelemetry-instrumentation-logging>=0.49b2",  # Logging integration
-    "opentelemetry-exporter-otlp-proto-grpc>=1.28.2",  # OTLP gRPC exporter
-    "python-json-logger>=3.2.0",  # Structured JSON logging
+    "prometheus-client>=0.21.0", # Prometheus metrics
+    "opentelemetry-api>=1.28.2", # OpenTelemetry API
+    "opentelemetry-sdk>=1.28.2", # OpenTelemetry SDK
+    "opentelemetry-instrumentation-asgi>=0.49b2", # Auto-instrument ASGI/Starlette
+    "opentelemetry-instrumentation-httpx>=0.49b2", # Auto-instrument httpx client
+    "opentelemetry-instrumentation-logging>=0.49b2", # Logging integration
+    "opentelemetry-exporter-otlp-proto-grpc>=1.28.2", # OTLP gRPC exporter
+    "python-json-logger>=3.2.0", # Structured JSON logging
 ]
 classifiers = [
     "Development Status :: 4 - Beta",

uv.lock

@@ -1053,7 +1053,7 @@ wheels = [
 
 [[package]]
 name = "nextcloud-mcp-server"
-version = "0.31.0"
+version = "0.31.1"
 source = { editable = "." }
 dependencies = [
     { name = "aiosqlite" },