Improve documentation (particularly on configuration) and the issue template

docs/02-usage/020_running.md

@@ -169,7 +169,7 @@ Some useful options include:
   * `--language-backend JetBrains`: use the Serena JetBrains Plugin as the language backend (overriding the default backend configured in the central configuration)
   * `--context <context>`: specify the operation [context](contexts) in which Serena shall operate
   * `--mode <mode>`: specify one or more [modes](modes) to enable (can be passed several times)
-  * `--enable-web-dashboard <true|false>`: enable or disable the web dashboard (enabled by default)
+  * `--open-web-dashboard <true|false>`: whether to open the web dashboard on startup (enabled by default)
 
 ## Other Commands
 

docs/02-usage/040_workflow.md

@@ -37,13 +37,34 @@ For instance, when using `uvx`, run
  * You can optionally specify a custom project name with `--name "My Project"`.
  * You can immediately index the project after creation with `--index`.
 
-After creation, you can adjust the project settings in the generated `.serena/project.yml` file.
+(project-config)=
+#### Project Configuration
+
+After creation, you can adjust the project settings in the generated `.serena/project.yml` file
+within the project directory.
+
+The file allows you to configure ...
+  * the set of programming languages for which language servers are spawned (not relevant when using the JetBrains plugin)  
+    Note that you can dynamically add/remove language servers while Serena is running via the [Dashboard](060_dashboard).
+  * the encoding used in source files
+  * ignore rules
+  * write access
+  * an initial prompt that shall be passed to the LLM whenever the project is activated 
+  * the name by which you want to refer to the project (relevant when telling the LLM to dynamically activate the project)
+
+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). 
 
 (indexing)=
 ### Indexing
 
-Especially for larger project, it is advisable to index the project after creation (in order to avoid
-delays during MCP server startup or the first tool application):
+:::{note}
+Indexing is not a relevant operation when using the JetBrains plugin, as indexing is handled by the IDE.
+:::
+
+Especially for larger project, it can be advisable to index the project after creation, pre-caching 
+symbol information provided by the language server(s). This will avoid delays during the first tool invocation
+that requires symbol information.
 
 While in the project directory, run this command:
    

docs/02-usage/050_configuration.md

@@ -1,38 +1,58 @@
 # Configuration
 
 Serena is very flexible in terms of configuration. While for most users, the default configurations will work,
-you can fully adjust it to your needs by editing a few yaml files. You can disable tools, change Serena's instructions
-(what we denote as the `system_prompt`), adjust the output of tools that just provide a prompt, and even adjust tool descriptions.
+you can fully adjust it to your needs.
 
-Serena is configured in four places:
+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.
 
-1. The `serena_config.yml` for general settings that apply to all clients and projects.
-   It is located in your user directory under `.serena/serena_config.yml`.
-   The file will be auto-generated when you first run Serena.
-   You can edit it directly or use
+Serena is configured in using a multi-layered approach:
 
-   ```shell
-   <serena> config edit
-   ```
+ * **global configuration** (`serena_config.yml`, see below)
+ * **project configuration** (`project.yml`, see [Project Configuration](project-config))
+ * **contexts and modes** for composable configuration, which can be enabled on a case-by-case basis (see below)
+ * **command-line parameters** passed to the `start-mcp-server` server command (overriding/extending configured settings)  
+   See [MCP Server Command-Line Arguments](mcp-args) for further information.  
+   
+## Global Configuration
 
-   where `<serena>` is [your way of running Serena](020_running).  
-   The configuration file can also be accessed through [Serena's dashboard](060_dashboard).
-2. In the arguments passed to the `start-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.
-   See for a detailed explanation. You can override all entries from the `serena_config.yml` through command line arguments.
-3. In the `.serena/project.yml` file within your project. This will hold project-level configuration that is used whenever
-   that project is activated. This file will be autogenerated when you first use Serena on that project, but you can also
-   create it explicitly with `serena project create [options]` (see the [](project-creation-indexing) 
-   for details on available options).
-4. Through the context and modes (see below).
+The global configuration file allows you to change general settings and defaults that will apply to all projects unless overridden.
 
-After the initial setup, continue with one of the sections below, depending on how you
-want to use Serena.
+### Settings
+
+Some of the configurable settings include:
+  * the language backend to use by default (i.e., the JetBrains plugin or language servers)
+  * UI settings affecting the [Serena Dashboard and GUI tool](060_dashboard.md)
+  * the set of tools to enable/disable by default
+  * tool execution parameters (timeout, max. answer length)
+  * global ignore rules
+  * logging settings
+  * advanced settings specific to individual language servers (see [below](ls-specific-settings))
+
+For detailed information on the parameters and possible settings, see the
+[template file](https://github.com/oraios/serena/blob/main/src/serena/resources/serena_config.template.yml).
+
+### Accessing the Configuration File
+
+The configuration file is auto-created when you first run Serena. It is stored in your user directory:
+  * Linux/macOS/Git-Bash: `~/.serena/serena_config.yml`
+  * Windows (CMD/PowerShell): `%USERPROFILE%\.serena\serena_config.yml`
+
+You can access it
+  * through [Serena's dashboard](060_dashboard) while Serena is running (use the respective button) 
+  * directly, using your favourite text editor
+  * using the command
+
+    ```shell
+    <serena> config edit
+    ```
+
+    where `<serena>` is [your way of running Serena](020_running).
 
 ## Modes and Contexts
 
-Serena's behavior and toolset can be adjusted using contexts and modes.
+Serena's behaviour and toolset can be adjusted using contexts and modes.
 These allow for a high degree of customization to best suit your workflow and the environment Serena is operating in.
 
 (contexts)=
@@ -134,7 +154,8 @@ For advanced users, Serena's configuration can be further customized.
 The Serena user data directory (where configuration, language server files, logs, etc. are stored) defaults to `~/.serena`.
 You can change this location by setting the `SERENA_HOME` environment variable to your desired path.
 
-### Language Server-Specific settings (`ls_specific_settings`)
+(ls-specific-settings)=
+### Language Server-Specific Settings
 
 Under the key `ls_specific_settings` in `serena_config.yml`, you can you pass per-language, 
 language server-specific configuration.