fix: Increase MCP sampling timeout to 5 minutes for slower LLMs

- Increase sampling timeout from 30s to 300s in semantic.py to accommodate
  slower local LLMs like Ollama
- Refactor RAG integration tests to support multiple providers (ollama,
  openai, anthropic, bedrock)
- Remove unnecessary embedding_provider fixture since MCP server handles
  embeddings internally
- Add --provider flag via tests/integration/conftest.py
- Add provider_fixtures.py with factory functions for generation providers

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

nextcloud_mcp_server/providers/anthropic.py

@@ -17,18 +17,20 @@ class AnthropicProvider(Provider):
     Note: Anthropic doesn't provide embedding models, only text generation.
     """
 
-    def __init__(self, api_key: str, model: str = "claude-3-5-sonnet-20241022"):
+    def __init__(
+        self, api_key: str, generation_model: str = "claude-3-5-sonnet-20241022"
+    ):
         """
         Initialize Anthropic provider.
 
         Args:
             api_key: Anthropic API key
-            model: Model name (e.g., "claude-3-5-sonnet-20241022")
+            generation_model: Model name (e.g., "claude-3-5-sonnet-20241022")
         """
         self.client = AsyncAnthropic(api_key=api_key)
-        self.model = model
+        self.model = generation_model
 
-        logger.info(f"Initialized Anthropic provider (model={model})")
+        logger.info(f"Initialized Anthropic provider (model={self.model})")
 
     @property
     def supports_embeddings(self) -> bool:

nextcloud_mcp_server/server/semantic.py

@@ -499,9 +499,11 @@ def configure_semantic_tools(mcp: FastMCP):
         )
 
         # 6. Request LLM completion via MCP sampling with timeout
+        # Note: 5 minute timeout to accommodate slower local LLMs (e.g., Ollama)
+        sampling_timeout_seconds = 300
 
         try:
-            with anyio.fail_after(30):
+            with anyio.fail_after(sampling_timeout_seconds):
                 sampling_result = await ctx.session.create_message(
                     messages=[
                         SamplingMessage(
@@ -548,14 +550,14 @@ def configure_semantic_tools(mcp: FastMCP):
 
         except TimeoutError:
             logger.warning(
-                f"Sampling request timed out after 30 seconds for query: '{query}', "
+                f"Sampling request timed out after {sampling_timeout_seconds} seconds for query: '{query}', "
                 f"returning search results only"
             )
             return SamplingSearchResponse(
                 query=query,
                 generated_answer=(
                     f"[Sampling request timed out]\n\n"
-                    f"The answer generation took too long (>30s). "
+                    f"The answer generation took too long (>{sampling_timeout_seconds}s). "
                     f"Found {len(accessible_results)} relevant documents. "
                     f"Please review the sources below or try a simpler query."
                 ),
@@ -675,15 +677,22 @@ def configure_semantic_tools(mcp: FastMCP):
             # Get Qdrant client and query indexed count
             indexed_count = 0
             try:
+                from qdrant_client.models import Filter
+
                 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
 
                 settings = get_settings()
                 qdrant_client = await get_qdrant_client()
 
-                # Count documents in collection
+                # Count documents in collection, excluding placeholders
+                # Placeholders are zero-vector points used to track processing state
                 count_result = await qdrant_client.count(
-                    collection_name=settings.get_collection_name()
+                    collection_name=settings.get_collection_name(),
+                    count_filter=Filter(must=[get_placeholder_filter()]),
                 )
                 indexed_count = count_result.count