Fix documentation configuration index

README.md

@@ -79,7 +79,7 @@ haiku-rag rebuild
 haiku-rag serve --monitor
 ```
 
-To customize settings, create a `haiku.rag.yaml` config file (see [Configuration](https://ggozad.github.io/haiku.rag/config-index/)).
+To customize settings, create a `haiku.rag.yaml` config file (see [Configuration](https://ggozad.github.io/haiku.rag/configuration/)).
 
 ## Python Usage
 
@@ -162,7 +162,7 @@ See the [examples directory](examples/) for working examples:
 Full documentation at: https://ggozad.github.io/haiku.rag/
 
 - [Installation](https://ggozad.github.io/haiku.rag/installation/) - Provider setup
-- [Configuration](https://ggozad.github.io/haiku.rag/config-index/) - YAML configuration
+- [Configuration](https://ggozad.github.io/haiku.rag/configuration/) - YAML configuration
 - [CLI](https://ggozad.github.io/haiku.rag/cli/) - Command reference
 - [Python API](https://ggozad.github.io/haiku.rag/python/) - Complete API docs
 - [Agents](https://ggozad.github.io/haiku.rag/agents/) - QA agent and multi-agent research

docs/cli.md

@@ -69,7 +69,7 @@ haiku-rag add-src /path/to/documents/
 ```
 
 !!! note
-    When adding a directory, the same content filters configured for [file monitoring](processing.md#filtering-monitored-files) are applied. This means `ignore_patterns` and `include_patterns` from your configuration will be used to filter which files are added.
+    When adding a directory, the same content filters configured for [file monitoring](configuration/processing.md#filtering-monitored-files) are applied. This means `ignore_patterns` and `include_patterns` from your configuration will be used to filter which files are added.
 
 !!! note
     As you add documents to `haiku.rag` the database keeps growing. By default, LanceDB supports versioning
@@ -158,7 +158,7 @@ haiku-rag research "How does haiku.rag organize and query documents?" --verbose
 Flags:
 - `--verbose`: Show planning, searching previews, evaluation summary, and stop reason
 
-Research parameters like `max_iterations`, `confidence_threshold`, and `max_concurrency` are configured in your [configuration file](config-index.md) under the `research` section.
+Research parameters like `max_iterations`, `confidence_threshold`, and `max_concurrency` are configured in your [configuration file](configuration/index.md) under the `research` section.
 
 When `--verbose` is set, the CLI consumes the research graph's AG-UI event stream, displaying step events and activity snapshots as agents progress through planning, search, evaluation, and synthesis. Without `--verbose`, only the final research report is displayed.
 

docs/configuration/index.md

@@ -3,7 +3,7 @@
 Configuration is done through YAML configuration files.
 
 !!! note
-    If you create a db with certain settings and later change them, `haiku.rag` will detect incompatibilities (for example, if you change embedding provider) and will exit. You can **rebuild** the database to apply the new settings, see [Rebuild Database](./cli.md#rebuild-database).
+    If you create a db with certain settings and later change them, `haiku.rag` will detect incompatibilities (for example, if you change embedding provider) and will exit. You can **rebuild** the database to apply the new settings, see [Rebuild Database](../cli.md#rebuild-database).
 
 ## Getting Started
 

docs/configuration/processing.md

@@ -92,7 +92,7 @@ conversion_options:
 
 - Offloads processing to docling-serve API
 - Better for heavy workloads and production
-- Requires docling-serve instance (see [Remote processing setup](remote-processing.md))
+- Requires docling-serve instance (see [Remote processing setup](../remote-processing.md))
 
 To use remote processing:
 

docs/configuration/qa-research.md

@@ -68,4 +68,4 @@ The server exposes:
 - `GET /health` - Health check endpoint
 - `POST /v1/agent/stream` - Research graph streaming endpoint (Server-Sent Events)
 
-See [Server Mode](server.md) for more details.
+See [Server Mode](../server.md) for more details.

docs/index.md

@@ -55,7 +55,7 @@ haiku-rag ask "Who is the author of haiku.rag?"
 
 - [Getting started](tutorial.md) - Tutorial
 - [Installation](installation.md) - Install haiku.rag with different providers
-- [Configuration](config-index.md) - Environment variables and settings
+- [Configuration](configuration/index.md) - Environment variables and settings
 - [CLI](cli.md) - Command line interface usage
 - [Server](server.md) - File monitoring and server mode
 - [MCP](mcp.md) - Model Context Protocol integration

docs/installation.md

@@ -43,7 +43,7 @@ The slim package has minimal dependencies and lets you install only what you nee
 - **OpenAI** (GPT models for QA and embeddings)
 - **Anthropic** (Claude models for QA)
 
-See [Configuration](config-index.md) for configuring providers including advanced options like vLLM.
+See [Configuration](configuration/index.md) for configuring providers including advanced options like vLLM.
 
 ## Requirements
 
@@ -71,7 +71,7 @@ When using `haiku.rag-slim`, you can skip installing the `docling` extra and ins
 - Offloading heavy document processing to a dedicated service
 - Production deployments with separate processing infrastructure
 
-See [Remote processing](remote-processing.md) for setup instructions and [Document Processing](processing.md) for configuration options.
+See [Remote processing](remote-processing.md) for setup instructions and [Document Processing](configuration/processing.md) for configuration options.
 
 ## Docker
 

docs/python.md

@@ -321,6 +321,6 @@ 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 are configured in `haiku.rag.yaml` or can be passed directly to the client (see [Configuration](config-index.md)).
+The QA provider and model are configured in `haiku.rag.yaml` or can be passed directly to the client (see [Configuration](configuration/index.md)).
 
 See also: [Agents](agents.md) for details on the QA agent and the multi‑agent research workflow.

docs/remote-processing.md

@@ -44,7 +44,7 @@ docker run -p 5001:5001 -e DOCLING_SERVE_ENABLE_UI=1 quay.io/docling-project/doc
 
 ### Configuration
 
-Configure haiku.rag to use docling-serve. See the [Document Processing](processing.md) guide for all available options.
+Configure haiku.rag to use docling-serve. See the [Document Processing](configuration/processing.md) guide for all available options.
 
 ```yaml
 # haiku.rag.yaml

docs/server.md

@@ -122,7 +122,7 @@ agui:
   cors_credentials: true
 ```
 
-See [Configuration](qa-research.md#ag-ui-server-configuration) for all available options.
+See [Configuration](configuration/qa-research.md#ag-ui-server-configuration) for all available options.
 
 ### Using the Streaming Endpoints
 

docs/tutorial.md

@@ -51,7 +51,7 @@ export OPENAI_API_KEY="<your OpenAI API key>"
 
 For the list of available OpenAI models and their vector dimensions, see the [OpenAI documentation](https://platform.openai.com/docs/guides/embeddings).
 
-See [Configuration](config-index.md) for all available options.
+See [Configuration](configuration/index.md) for all available options.
 
 ## Adding the first documents
 
@@ -216,4 +216,4 @@ The following people are presenting talks at PyCon Finland 2025:
 
 ## Configuration
 
-See [Configuration page](./config-index.md) for complete documentation on YAML configuration and all available options.
+See [Configuration page](./configuration/index.md) for complete documentation on YAML configuration and all available options.

mkdocs.yml

@@ -60,11 +60,11 @@ nav:
       - Getting started: tutorial.md
       - Installation: installation.md
       - Configuration:
-          - config-index.md
-          - Providers: providers.md
-          - QA and Research: qa-research.md
-          - Document Processing: processing.md
-          - Storage: storage.md
+          - configuration/index.md
+          - Providers: configuration/providers.md
+          - QA and Research: configuration/qa-research.md
+          - Document Processing: configuration/processing.md
+          - Storage: configuration/storage.md
       - CLI: cli.md
       - Python: python.md
       - Agents: agents.md