Readme, docs: clarified config file creation and JB plugin role

Also added a sentence on using with the Codex app

README.md

@@ -47,7 +47,8 @@ complex projects!
 
 There are two alternative technologies powering these capabilities:
 
-* **Language servers** implementing the language server Protocol (LSP) — the free/open-source alternative.
+* **Language servers** implementing the language server Protocol (LSP) — the free/open-source alternative 
+  which is used by default.
 * The **Serena JetBrains Plugin**, which leverages the powerful code analysis and editing
   capabilities of your JetBrains IDE (paid plugin; free trial available).
 
@@ -180,16 +181,21 @@ https://github.com/user-attachments/assets/6eaa9aa1-610d-4723-a2d6-bf1e487ba753
 > [!NOTE]
 > When using the language server backend, some additional dependencies to be installed for certain languages; see the [Language Support](https://oraios.github.io/serena/01-about/020_programming-languages.html) page for details.
 
-**Starting the MCP Server**. The easiest way to start the Serena MCP server is by running the latest version from GitHub using uvx.  
-Issue this command to see available options:
+**Starting the MCP Server**. The easiest way to start the Serena MCP server is by running the latest version from GitHub using uvx:
 
 ```bash
-uvx -p 3.13 --from git+https://github.com/oraios/serena serena start-mcp-server --help
+uvx -p 3.13 --from git+https://github.com/oraios/serena serena start-mcp-server
 ```
 
+If this is the first time you are starting Serena, the necessary configuration files will be created, and 
+you should see the Serena dashboard appear. You can terminate the server by pressing Ctrl+C (multiple times, if necessary).
+
 **Configuring Your Client**. To connect Serena to your preferred MCP client, you typically need to [configure a launch command in your client](https://oraios.github.io/serena/02-usage/030_clients.html).
 Follow the link for specific instructions on how to set up Serena for Claude Code, Codex, Claude Desktop, MCP-enabled IDEs and other clients (such as local and web-based GUIs). 
 
+**Switching to the JetBrains Backend**. The default code intelligence backend for Serena is the free LSP backend.
+For using the more powerful JetBrains backend, follow the instructions on the [JetBrains Plugin page](https://oraios.github.io/serena/02-usage/025_jetbrains_plugin.html).
+
 > [!TIP]
 > While getting started quickly is easy, Serena is a powerful toolkit with many configuration options.
 > We highly recommend reading through the [user guide](https://oraios.github.io/serena/02-usage/000_intro.html) to get the most out of Serena.

docs/02-usage/025_jetbrains_plugin.md

@@ -1,7 +1,11 @@
 # The Serena JetBrains Plugin
 
-The [JetBrains Plugin](https://plugins.jetbrains.com/plugin/28946-serena/) allows Serena to
+The [JetBrains Plugin](https://plugins.jetbrains.com/plugin/28946-serena/) allows the Serena MCP server to
 leverage the powerful code analysis and editing capabilities of your JetBrains IDE.
+This page explains how to install the plugin and how to configure Serena for using it. 
+You will still need to set up the Serena MCP server 
+itself, so make sure to follow the [installation instructions](020_running.md) and connect the MCP server to your 
+LLM-based client as described in [client setup](030_clients.md) in addition to following the instructions below.
 
 ```{raw} html
 <p>
@@ -61,9 +65,18 @@ After installing the plugin, you need to configure Serena to use it.
 
 **Central Configuration**.
 
-Edit the global Serena configuration file located at `~/.serena/serena_config.yml` 
+If you ever executed Serena before, you will have the global Serena configuration file located at `~/.serena/serena_config.yml` 
 (`%USERPROFILE%\.serena\serena_config.yml` on Windows).
-Change the `language_backend` setting as follows:
+
+If the configuration file does not exist, run
+
+```shell
+uvx -p 3.13 --from git+https://github.com/oraios/serena serena start-mcp-server
+```
+
+(see [running Serena](020_running.md) for alternative options) to install all dependencies and create configuration files. Terminate the server with `Ctrl+C` after it has started.
+
+In your configuration, change the `language_backend` setting as follows:
 
 ```yaml
 language_backend: JetBrains

docs/02-usage/030_clients.md

@@ -147,7 +147,7 @@ While serena can be directly installed from the GitHub MCP server registry, we r
 
 ## Codex
 
-Serena works with OpenAI's Codex CLI out of the box, but you have to use the `codex` context for it to work properly. (The technical reason is that Codex doesn't fully support the MCP specifications, so some massaging of tools is required.).
+Serena works with OpenAI's Codex CLI and app out of the box, but you have to use the `codex` context for it to work properly. (The technical reason is that Codex doesn't fully support the MCP specifications, so some massaging of tools is required.).
 
 Add a [run command](020_running) to `~/.codex/config.toml` to configure Serena for all Codex sessions;
 create the file if it does not exist.
@@ -162,6 +162,12 @@ args = ["-p", "3.13", "--from", "git+https://github.com/oraios/serena", "serena"
 
 The larger startup timeout is to permit uvx to download the necessary dependencies. Once downloaded, the startup time is much faster.
 
+:::{note}
+The codex app does not start a session in the project's directory, so when using the app, you will have to 
+ask Codex to "Activate the current dir as project using serena" at the start of each session. 
+This is not necessary when using the codex CLI.
+:::
+
 :::{attention}
 Codex currently ignores the [instructions](https://blog.modelcontextprotocol.io/posts/2025-11-03-using-server-instructions/) 
 property of MCP servers, so it is recommended to prompt the agent to