Docs: Refresh docs to organize and standardize reference materials. (#18403)

docs/get-started/configuration.md

@@ -1374,10 +1374,9 @@ for that specific session.
   - Specifies the Gemini model to use for this session.
   - Example: `npm start -- --model gemini-3-pro-preview`
 - **`--prompt <your_prompt>`** (**`-p <your_prompt>`**):
+  - **Deprecated:** Use positional arguments instead.
   - Used to pass a prompt directly to the command. This invokes Gemini CLI in a
     non-interactive mode.
-  - For scripting examples, use the `--output-format json` flag to get
-    structured output.
 - **`--prompt-interactive <your_prompt>`** (**`-i <your_prompt>`**):
   - Starts an interactive session with the provided prompt as the initial input.
   - The prompt is processed within the interactive session, not before it.