Move tool list to docs, restructure README

docs/01-about/035_tools.md

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+## List of Tools
+
+Find the full list of Serena's tools below (output of `<serena> tools list --all`).
+
+Note that in most configurations, only a subset of these tools will be enabled simultaneously (see the section on [configuration](../02-usage/050_configuration) for details).
+
+* `activate_project`: Activates a project based on the project name or path.
+* `check_onboarding_performed`: Checks whether project onboarding was already performed.
+* `create_text_file`: Creates/overwrites a file in the project directory.
+* `delete_lines`: Deletes a range of lines within a file.
+* `delete_memory`: Deletes a memory from Serena's project-specific memory store.
+* `execute_shell_command`: Executes a shell command.
+* `find_file`: Finds files in the given relative paths
+* `find_referencing_symbols`: Finds symbols that reference the symbol at the given location (optionally filtered by type).
+* `find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (optionally filter
+  ed by type).
+* `get_current_config`: Prints the current configuration of the agent, including the active and available projects, tools,
+  contexts, and modes.
+* `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file.
+* `initial_instructions`: Provides instructions on how to use the Serena toolbox.
+* `insert_after_symbol`: Inserts content after the end of the definition of a given symbol.
+* `insert_at_line`: Inserts content at a given line in a file.
+* `insert_before_symbol`: Inserts content before the beginning of the definition of a given symbol.
+* `jet_brains_find_referencing_symbols`: Finds symbols that reference the given symbol
+* `jet_brains_find_symbol`: Performs a global (or local) search for symbols with/containing a given name/substring (option
+  ally filtered by type).
+* `jet_brains_get_symbols_overview`: Retrieves an overview of the top-level symbols within a specified file
+* `list_dir`: Lists files and directories in the given directory (optionally with recursion).
+* `list_memories`: Lists memories in Serena's project-specific memory store.
+* `onboarding`: Performs onboarding (identifying the project structure and essential tasks, e.g. for testing or building).
+* `prepare_for_new_conversation`: Provides instructions for preparing for a new conversation (in order to continue with th
+  e necessary context).
+* `read_file`: Reads a file within the project directory.
+* `read_memory`: Reads the memory with the given name from Serena's project-specific memory store.
+* `remove_project`: Removes a project from the Serena configuration.
+* `rename_symbol`: Renames a symbol throughout the codebase using language server refactoring capabilities.
+* `replace_lines`: Replaces a range of lines within a file with new content.
+* `replace_regex`: Replaces content in a file by using regular expressions.
+* `replace_symbol_body`: Replaces the full definition of a symbol.
+* `restart_language_server`: Restarts the language server, may be necessary when edits not through Serena happen.
+* `search_for_pattern`: Performs a search for a pattern in the project.
+* `summarize_changes`: Provides instructions for summarizing the changes made to the codebase.
+* `switch_modes`: Activates modes by providing a list of their names
+* `think_about_collected_information`: Thinking tool for pondering the completeness of collected information.
+* `think_about_task_adherence`: Thinking tool for determining whether the agent is still on track with the current task.
+* `think_about_whether_you_are_done`: Thinking tool for determining whether the task is truly completed.
+* `write_memory`: Writes a named memory (for future reference) to Serena's project-specific memory store.