Improve docs

docs/02-usage/040_workflow.md

@@ -13,7 +13,7 @@ setting up a project with Serena typically involves the following steps:
 4. **Working on coding tasks**: Using Serena to help you with actual coding tasks in the project
 
 (project-creation-indexing)=
-## Project Creation & Indexing
+## Project Creation
 
 Project creation is the process of defining fundamental project settings that are relevant to Serena's operation.
 
@@ -38,7 +38,7 @@ To explicitly create a project, use the following command while in the project d
  * You can immediately index the project after creation with `--index`.
 
 (project-config)=
-#### Project Configuration
+## Project Configuration
 
 After creation, you can adjust the project settings in the generated `.serena/project.yml` file
 within the project directory.
@@ -61,17 +61,17 @@ For detailed information on the parameters and possible settings, see the
 [template file](https://github.com/oraios/serena/blob/main/src/serena/resources/project.template.yml).
 
 :::{note}
-Many settings in project.yml *extend* or *override* settings in the global configuration file `serena_config.yml`.
+Many settings in project.yml *extend* or *override* settings in [Serena's global configuration](global-config).
 So use the project configuration specifically for aspects that apply only to the particular project.
 :::
 
-**Local Overrides**. The project.yml file is intended to be versioned together with the project.
+**Local Overrides**. The `project.yml` file is intended to be versioned together with the project.
 You can specify local overrides for the settings in a `project.local.yml` file in the same directory
 (which, by default, is ignored by git). 
 Any keys defined therein will override the respective key in `project.yml`.
 
 (indexing)=
-### Indexing
+## Indexing
 
 :::{note}
 Indexing is not a relevant operation when using the JetBrains plugin, as indexing is handled by the IDE.
@@ -83,7 +83,7 @@ that requires symbol information.
 
 While in the project directory, run this command:
    
-    <serena> project index
+    serena project index
 
 Indexing has to be called only once. During regular usage, Serena will automatically update the index whenever files change.
 

docs/02-usage/050_configuration.md

@@ -7,7 +7,7 @@ You can disable tools, change Serena's fundamental instructions
 (what we denote as the `system_prompt`), adjust the output of tools that just provide a prompt, 
 and even adjust tool descriptions.
 
-Serena is configured in using a multi-layered approach:
+Serena is configured using a multi-layered approach:
 
  * **global configuration** (`serena_config.yml`, see below)
  * **project configuration** (`project.yml`, see [Project Configuration](project-config))