docs: add prompts, tools, and settings documentation

Add custom prompts documentation, tools configuration guide, and
settings reference. Add design document for custom prompts and tools
RFC. Update README with tools and prompts configuration sections.

Signed-off-by: derekbarbosa <derekasobrab@gmail.com>

Author: derekbarbosa

README.md

@@ -90,6 +90,8 @@ Copy `Settings.toml` to customize your configuration. The default `Settings.toml
 *   **Server**: API server host and port.
 *   **Git**: Path to the reference kernel repository.
 *   **Review**: Concurrency and worktree settings.
+    *   **Tools**: Configure which AI tools are enabled (optional). See [docs/TOOLS.md](docs/TOOLS.md) for details.
+    *   **Prompts**: Customize review stages and prompts (optional). See [docs/PROMPTS.md](docs/PROMPTS.md) for details.
 
 #### Configuring the LLM Provider
 
@@ -125,7 +127,7 @@ gemini skills install ./skills/sashiko-feature.skill --scope workspace
 
 For users of other agent interfaces (e.g., OpenCode, Claude Code), we recommend following your interface's specific settings to symlink or copy the skill configurations (the `SKILL.md` and `references/` files) into your agent's custom instruction path.
 
-You can also configure settings via environment variables using the `SASHIKO` prefix and `__` (double underscore) as the separator between every segment (e.g., `SASHIKO__AI__PROVIDER=gemini`).
+You can also configure settings via environment variables using the `SASHIKO` prefix and double underscores for nesting (e.g., `SASHIKO__AI__PROVIDER=gemini`).
 
 **Important**: You must set the `LLM_API_KEY` environment variable with your provider's API key.
 ```bash