Use ~/.serena/serena_config.yml as the only location for the config file,

adding a migration for old files in the Serena directory

README.md

@@ -201,11 +201,15 @@ This and other settings can be adjusted in the [configuration](#configuration) a
    git clone https://github.com/oraios/serena
    cd serena
    ```
-2. Optionally create a config file from the template and adjust it according to your preferences.
-   You can either place it in your user directory (`~/.serena/serena_config.yml`) or into 
-   the Serena installation directory:
+2. Optionally create the configuration file in your home directory, i.e.
+
+      * `~/.serena/serena_config.yml` on Linux and macOS, or
+      * `%USERPROFILE%\.serena\serena_config.yml` on Windows.  
+
+   by copying the template and then adjusting it according to your needs:   
    ```shell
-   cp src/serena/resources/serena_config.template.yml serena_config.yml
+   mkdir ~/.serena
+   cp src/serena/resources/serena_config.template.yml ~/.serena/serena_config.yml
    ```
    If you just want the default config, you can skip this part, and a config file will be created when you first run Serena.
 3. Run the server with `uv`:
@@ -282,10 +286,8 @@ Run with parameter `--help` to get a list of available options.
 Serena's behavior (active tools and prompts as well as logging configuration, etc.) is configured in four places:
 
 1. The `serena_config.yml` for general settings that apply to all clients and projects.
-   Serena will look for this file in your user directory under `.serena/serena_config.yml`
-   or within the Serena installation directory.
-   If you do not explicitly create the file, it will be auto-generated in the former location
-   when you first run Serena.
+   It is located in your user directory under `.serena/serena_config.yml`.
+   If you do not explicitly create the file, it will be auto-generated when you first run Serena.
 2. In the arguments passed to the `serena-mcp-server` in your client's config (see below), 
    which will apply to all sessions started by the respective client. In particular, the [context](#contexts) parameter
    should be set appropriately for Serena to be best adjusted to existing tools and capabilities of your client.

src/serena/config/serena_config.py

@@ -245,14 +245,15 @@ class SerenaConfig:
         if is_running_in_docker():
             return os.path.join(REPO_ROOT, cls.CONFIG_FILE_DOCKER)
         else:
-            candidates = [
-                str(Path.home() / SERENA_MANAGED_DIR_NAME / cls.CONFIG_FILE),
-                os.path.join(REPO_ROOT, cls.CONFIG_FILE),
-            ]
-            for candidate in candidates:
-                if os.path.exists(candidate):
-                    return candidate
-            return candidates[0]
+            config_path = str(Path.home() / SERENA_MANAGED_DIR_NAME / cls.CONFIG_FILE)
+
+            # migrate configuration in old location
+            old_config_path = os.path.join(REPO_ROOT, cls.CONFIG_FILE)
+            if os.path.exists(old_config_path):
+                log.info(f"Moving Serena configuration file from {old_config_path} to {config_path}")
+                shutil.move(old_config_path, config_path)
+
+            return config_path
 
     @classmethod
     def from_config_file(cls, generate_if_missing: bool = True) -> "SerenaConfig":