Remove docs references to env vars

docs/python.md

@@ -222,6 +222,6 @@ answer = await client.ask(
 
 The QA agent will search your documents for relevant information and use the configured LLM to generate a comprehensive answer. With `cite=True`, responses include citations showing which documents were used as sources. Citations prefer the document title when present, otherwise they use the URI.
 
-The QA provider and model can be configured via environment variables (see [Configuration](configuration.md)).
+The QA provider and model are configured in `haiku.rag.yaml` or can be passed directly to the client (see [Configuration](configuration.md)).
 
 See also: [Agents](agents.md) for details on the QA agent and the multi‑agent research workflow.

docs/server.md

@@ -45,11 +45,19 @@ This will start file monitoring, MCP server on port 8001, and A2A server on port
 
 ## File Monitoring
 
-Set `MONITOR_DIRECTORIES` environment variable to enable automatic file monitoring:
+Configure directories to monitor in your `haiku.rag.yaml`:
+
+```yaml
+storage:
+  monitor_directories:
+    - /path/to/documents
+    - /another/path
+```
+
+Then start the server:
 
 ```bash
-export MONITOR_DIRECTORIES="/path/to/documents"
-haiku-rag serve
+haiku-rag serve --monitor
 ```
 
 ### Monitoring Features

docs/tutorial.md

@@ -225,6 +225,4 @@ rm -rf "/Users/moo/Library/Application Support/haiku.rag/haiku.rag.lancedb"
 
 ## Configuration
 
-See [Configuration page](./configuration.md) for more information about configuration
-
-For the available environment variable config options see [config.py](https://github.com/ggozad/haiku.rag/blob/main/src/haiku/rag/config.py).
+See [Configuration page](./configuration.md) for complete documentation on YAML configuration and all available options.