Add/improve docs on security

docs/02-usage/070_security.md

@@ -0,0 +1,12 @@
+## Security Considerations
+
+As fundamental abilities for a coding agent, Serena contains tools for executing shell commands and modifying files.
+Therefore, if the respective tool calls are not monitored or restricted (and execution takes place in a sensitive environment), 
+there is a risk of unintended consequences.
+
+Therefore, to reduce the risk of unintended consequences when using Serena, it is recommended to
+  * back up your work regularly (e.g. use a version control system like Git),
+  * monitor tool executions carefully (e.g. via your MCP client, provided that it supports it),
+  * consider enabling read-only mode for your project (set `read_only: True` in project.yml) if you only want to analyze code without modifying it,
+  * restrict the set of allowed tools via the [configuration](050_configuration),
+  * use a sandboxed environment for running Serena (e.g. by [using Docker](020_running.md#using-docker-experimental)).

docs/02-usage/999_detailed-usage.md

@@ -10,26 +10,6 @@ The use of all tools is generally recommended, as this allows Serena to provide
 Only by executing shell commands (in particular, tests) can Serena identify and correct mistakes
 autonomously.
 
-#### Shell Execution and Editing Tools
-
-Many clients have their own shell execution tool, and by default Serena's shell tool will be disabled in them
-(e.g., when using the `ide-assistant` or `codex` context). However, when using Serena through something like
-Claude Desktop or ChatGPT, it is recommended to enable Serena's `execute_shell_command` tool to allow
-agentic behavior.
-
-It should be noted that the `execute_shell_command` tool allows for arbitrary code execution.
-When using Serena as an MCP Server, clients will typically ask the user for permission
-before executing a tool, so as long as the user inspects execution parameters beforehand,
-this should not be a problem.
-However, if you have concerns, you can choose to disable certain commands in your project's configuration file.
-If you only want to use Serena purely for analyzing code and suggesting implementations
-without modifying the codebase, you can enable read-only mode by setting `read_only: true` in your project configuration file.
-This will automatically disable all editing tools and prevent any modifications to your codebase while still
-allowing all analysis and exploration capabilities.
-
-In general, be sure to back up your work and use a version control system in order to avoid
-losing any work.
-
 ### Prepare Your Project
 
 #### Structure Your Codebase