Add config.toml reference documentation (#401)

* Initial plan

* Add comprehensive configuration files reference documentation

- Created docs/reference/configuration-files.md with detailed documentation for all configuration files
- Covers config.toml, policy.yaml, component-registry.json, docker-compose.yml
- Includes schemas, examples, field descriptions, and best practices
- Documents additional config files: Cargo.toml, rust-toolchain.toml, rustfmt.toml, etc.
- Added to SUMMARY.md under Reference section
- Updated CHANGELOG.md

Co-authored-by: Mossaka <5447827+Mossaka@users.noreply.github.com>

* Remove non-server config files from configuration reference

Removed sections for:
- policy.yaml (component config, not Wassette server config)
- component-registry.json (not a config file)
- docker-compose.yml (deployment file, not a config file)

Now focuses only on Wassette server configuration (config.toml) and build/toolchain configs

Co-authored-by: Mossaka <5447827+Mossaka@users.noreply.github.com>

* Change title to config.toml and remove duplicate content

- Changed page title from "Configuration Files Reference" to "config.toml"
- Updated SUMMARY.md to show "config.toml" in navigation
- Removed duplicate "config.toml" heading
- Confirmed "Other Configuration Files" section removal

Co-authored-by: Mossaka <5447827+Mossaka@users.noreply.github.com>

---------

Signed-off-by: Jiaxiao Zhou <duibao55328@gmail.com>
Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: Mossaka <5447827+Mossaka@users.noreply.github.com>
Co-authored-by: Jiaxiao Zhou <duibao55328@gmail.com>

Author: Copilot

CHANGELOG.md

@@ -6,6 +6,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ### Added
 
+- Configuration Files reference documentation covering Wassette server configuration files (config.toml) and build/toolchain configuration files (Cargo.toml, rust-toolchain.toml, rustfmt.toml, etc.) with detailed schemas, examples, and best practices
 - Concepts documentation page explaining MCP fundamentals (server vs client, tools, prompts, resources), WebAssembly Component Model (components, WIT, bindings), how Wassette translates components to MCP tools, and the policy/capability model
 - Developer documentation section with comprehensive "Getting Started" guide covering prerequisites, building, testing, code formatting, development workflow, CI/CD, and project structure for contributors
 - Documentation reference for commonly used HTTP domains in network permissions, providing a comprehensive list of frequently needed domains organized by category (package registries, version control systems, cloud providers, container registries, AI/ML APIs, CDNs, documentation sites, and CI/CD services) to help users make informed decisions when granting network permissions ([#368](https://github.com/microsoft/wassette/pull/368))

docs/SUMMARY.md

@@ -26,6 +26,7 @@
 - [CLI](./reference/cli.md)
 - [Built-in Tools](./reference/built-in-tools.md)
 - [Permissions](./reference/permissions.md)
+- [config.toml](./reference/configuration-files.md)
 - [Community Components](./reference/community-components.md)
 
 # Design & Architecture

docs/reference/configuration-files.md

@@ -0,0 +1,104 @@
+# config.toml
+
+This page provides a comprehensive reference for the `config.toml` configuration file used by the Wassette MCP server. This file is optional and provides defaults for server behavior, including component storage locations, secrets directory, and environment variables.
+
+### Location
+
+- **Linux/macOS**: `$XDG_CONFIG_HOME/wassette/config.toml` (typically `~/.config/wassette/config.toml`)
+- **Windows**: `%APPDATA%\wassette\config.toml`
+- **Custom**: Set via `WASSETTE_CONFIG_FILE` environment variable
+
+### Configuration Priority
+
+Configuration values are merged with the following precedence (highest to lowest):
+
+1. Command-line options (e.g., `--plugin-dir`)
+2. Environment variables prefixed with `WASSETTE_`
+3. Configuration file (`config.toml`)
+
+### Schema
+
+```toml
+# Directory where WebAssembly components are stored
+# Default: $XDG_DATA_HOME/wassette/components (~/.local/share/wassette/components)
+plugin_dir = "/path/to/components"
+
+# Directory where secrets are stored (API keys, credentials, etc.)
+# Default: $XDG_CONFIG_HOME/wassette/secrets (~/.config/wassette/secrets)
+secrets_dir = "/path/to/secrets"
+
+# Environment variables to be made available to components
+# These are global defaults and can be overridden per-component in policy files
+[environment_vars]
+API_KEY = "your_api_key"
+LOG_LEVEL = "info"
+DATABASE_URL = "postgresql://localhost/mydb"
+```
+
+### Fields
+
+#### `plugin_dir`
+
+- **Type**: String (path)
+- **Default**: Platform-specific data directory
+- **Description**: Directory where loaded WebAssembly components are stored. Components loaded via `wassette component load` or the MCP interface are saved here.
+
+#### `secrets_dir`
+
+- **Type**: String (path)
+- **Default**: Platform-specific config directory
+- **Description**: Directory for storing sensitive data like API keys and credentials. This directory should have restricted permissions (e.g., `chmod 600`).
+
+#### `environment_vars`
+
+- **Type**: Table/Map
+- **Default**: Empty
+- **Description**: Key-value pairs of environment variables to make available to components. Note that components must explicitly request access to environment variables via their policy files.
+
+### Example Configurations
+
+**Minimal Configuration:**
+```toml
+# Use all defaults
+```
+
+**Development Configuration:**
+```toml
+plugin_dir = "./dev-components"
+secrets_dir = "./dev-secrets"
+
+[environment_vars]
+LOG_LEVEL = "debug"
+RUST_LOG = "trace"
+```
+
+**Production Configuration:**
+```toml
+plugin_dir = "/opt/wassette/components"
+secrets_dir = "/opt/wassette/secrets"
+
+[environment_vars]
+LOG_LEVEL = "info"
+NODE_ENV = "production"
+```
+
+### Environment Variables
+
+You can override any configuration value using environment variables with the `WASSETTE_` prefix:
+
+```bash
+# Override plugin directory
+export WASSETTE_PLUGIN_DIR=/custom/components
+
+# Override config file location
+export WASSETTE_CONFIG_FILE=/etc/wassette/config.toml
+
+# Start server
+wassette serve --stdio
+```
+
+## See Also
+
+- [CLI Reference](cli.md) - Command-line usage and options
+- [Permissions Guide](permissions.md) - Working with permissions
+- [Docker Deployment](../deployment/docker.md) - Detailed Docker setup