Add reference documentation

docs/ref/configuration/README.md

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-# Configuration

docs/ref/configuration/configuration-files.md

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-# Configuration files
+# Configuration files
+
+### 1. Wazuh Manager Configuration
+
+* **`ossec.conf`**: The main configuration file for the Wazuh manager. It controls rules, decoders, agent enrollment, active responses, integrations, clustering, and more.
+    * **Customization**: Mount a custom `ossec.conf` or specific configuration snippets (e.g., local rules in `local_rules.xml`) into the manager container at `/wazuh-mount-point/`, which will be copied to the path `/var/ossec` (e.g., the file `/var/ossec/etc/ossec.conf` must be mounted at `/wazuh-mount-point/etc/ossec.conf`) .
+
+### 2. Wazuh Indexer Configuration
+
+* **`opensearch.yml`**: The primary configuration file for OpenSearch. Controls cluster settings, network binding, path settings, discovery, memory allocation, etc.
+    * **Customization**: Mount a custom `opensearch.yml` into the indexer container(s) at `/usr/share/wazuh-indexer/config/opensearch.yml`.
+* **JVM Settings (`jvm.options`)**: Manages Java Virtual Machine settings, especially heap size (`-Xms`, `-Xmx`). Critical for performance and stability.
+    * **Customization**: Mount a custom `jvm.options` file or set `OPENSEARCH_JAVA_OPTS` environment variable.
+
+### 3. Wazuh Dashboard (OpenSearch Dashboards) Configuration
+
+* **`opensearch_dashboards.yml`**: The main configuration file for OpenSearch Dashboards. Controls server host/port, OpenSearch connection URL, SSL settings, and Wazuh plugin settings.
+    * **Customization**: Mount a custom `opensearch_dashboards.yml` into the dashboard container at `/usr/share/wazuh-dashboard/config/opensearch_dashboards.yml` and custom `wazuh.yml` into the dashboard container at `/usr/share/wazuh-dashboard/data/wazuh/config/wazuh.yml` .
+* **Wazuh Plugin Settings**: The Wazuh plugin for the dashboard has its own configuration, often within `opensearch_dashboards.yml` or managed through environment variables, specifying the Wazuh API URL and credentials.
+
+## Applying Configuration Changes
+
+1.  **Modify `docker-compose.yml`**:
+    * For changes to environment variables, port mappings, or volume mounts.
+    * After changes, you typically need to stop and restart the containers:
+        ```bash
+        docker compose down
+        docker compose up -d
+        ```
+
+
+Consult the official Wazuh documentation for version 4.12.2 for detailed information on all possible configuration parameters for each component.

docs/ref/configuration/configuration.md

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+# Reference Manual - Configuration
+
+This section details how to configure your Wazuh-Docker deployment (version 4.12.0). Proper configuration is key to tailoring the Wazuh stack to your specific needs, managing data persistence, and integrating with your environment.
+
+## Overview of Configuration Methods
+
+Configuring Wazuh components within a Docker environment typically involves several methods:
+
+1.  **[Environment Variables](environment-variables.md)**:
+    * Many container settings are controlled by passing environment variables at runtime (e.g., via the `docker-compose.yml` file or `docker run` commands).
+    * These are often used for setting up initial passwords, component versions, cluster names, or basic operational parameters.
+
+2.  **[Configuration Files](configuration-files.md)**:
+    * Core Wazuh components (manager, indexer, dashboard) rely on their traditional configuration files (e.g., `ossec.conf`, `opensearch.yml`, `opensearch_dashboards.yml`).
+    * To customize these, you typically mount your custom configuration files into the containers, replacing or supplementing the defaults. This is managed using Docker volumes in your `docker-compose.yml`.
+
+3.  **Docker Compose File (`docker-compose.yml`)**:
+    * The `docker-compose.yml` file itself is a primary configuration tool. It defines:
+        * Which services (containers) to run.
+        * The Docker images to use.
+        * Port mappings.
+        * Volume mounts for persistent data and custom configurations.
+        * Network configurations.
+        * Resource limits (CPU, memory).
+        * Dependencies between services.
+
+4.  **Persistent Data Volumes**:
+    * Configuration related to data storage (e.g., paths for Wazuh Indexer data, Wazuh manager logs and agent keys) is managed through Docker volumes. Persisting these volumes ensures your data and critical configurations survive container restarts or recreations.

docs/ref/configuration/environment-variables.md

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-# Environment Variables
+# Environment Variabless