Deleted obsolete tools. Essentially backwards compatible

Enhanced tool registry check to log a warning instead of crashing when
a deleted tool name is passed

.serena/project.yml

@@ -48,41 +48,41 @@ read_only: false
 # Below is the complete list of tools for convenience.
 # To make sure you have the latest list of tools, and to view their descriptions, 
 # execute `uv run scripts/print_tool_overview.py`.
-#
-#  * `activate_project`: Activates a project by name.
+#  * `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.
+#  * `delete_memory`: Delete a memory file. Should only happen if a user asks for it explicitly,
+#       for example by saying that the information retrieved from a memory file is no longer correct
+#       or no longer relevant for the project.
+#  * `edit_memory`: Replaces content matching a regular expression in a memory.
 #  * `execute_shell_command`: Executes a shell command.
-#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
-#  * `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 filtered by type).
+#  * `find_file`: Finds files in the given relative paths
+#  * `find_referencing_symbols`: Finds symbols that reference the given symbol using the language server backend
+#  * `find_symbol`: Performs a global (or local) search using the language server backend.
 #  * `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`: Gets the initial instructions for the current project.
-#     Should only be used in settings where the system prompt cannot be set,
-#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `initial_instructions`: Provides instructions Serena usage (i.e. the 'Serena Instructions Manual')
+#       for clients that do not read the initial instructions when the MCP server is connected.
 #  * `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.
 #  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
-#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `list_memories`: List available memories. Any memory can be read using the `read_memory` tool.
 #  * `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 the 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.
-#  * `replace_lines`: Replaces a range of lines within a file with new content.
-#  * `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.
+#  * `read_memory`: Read the content of a memory file. This tool should only be used if the information
+#       is relevant to the current task. You can infer whether the information
+#       is relevant from the memory file name.
+#       You should not read the same memory file multiple times in the same conversation.
+#  * `rename_memory`: Renames or moves a memory. Moving between project and global scope is supported
+#       (e.g., renaming "global/foo" to "bar" moves it from global to project scope).
+#  * `rename_symbol`: Renames a symbol throughout the codebase using language server refactoring capabilities.
+#       For JB, we use a separate tool.
+#  * `replace_content`: Replaces content in a file (optionally using regular expressions).
+#  * `replace_symbol_body`: Replaces the full definition of a symbol using the language server backend.
+#  * `safe_delete_symbol`:
 #  * `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.
+#  * `write_memory`: Write some information (utf-8-encoded) about this project that can be useful for future tasks to a memory in md format.
+#       The memory name should be meaningful.
 excluded_tools: []
 
 # list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).

docs/02-usage/050_configuration.md

@@ -145,10 +145,6 @@ If you want to keep certain modes as always active, regardless of command-line p
 define them as *base modes* in the global or project configuration.
 :::
 
-Modes can also be _switched dynamically_ during a session. 
-You can instruct the LLM to use the `switch_modes` tool to activate a different set of modes (e.g., "Switch to planning and one-shot modes").
-Like command-line parameters, this only affects default modes, not base modes (which remain active).
-
 :::{note}
 **Mode Compatibility**: While you can combine modes, some may be semantically incompatible (e.g., `interactive` and `one-shot`). 
 Serena currently does not prevent incompatible combinations; it is up to the user to choose sensible mode configurations.

src/serena/agent.py

@@ -146,24 +146,20 @@ class ToolSet:
                 tool_names = set()
                 for fixed_tool in definition.fixed_tools:
                     fixed_tool = get_updated_tool_name(fixed_tool)
-                    if not registry.is_valid_tool_name(fixed_tool):
-                        raise ValueError(f"Invalid tool name '{fixed_tool}' provided for fixed tool set")
-                    tool_names.add(fixed_tool)
+                    if registry.check_valid_tool_name(fixed_tool, " (in fixed tools set)"):
+                        tool_names.add(fixed_tool)
                 log.info(f"{definition} defined a fixed tool set with {len(tool_names)} tools: {', '.join(tool_names)}")
             else:
                 included_tools = []
                 excluded_tools = []
                 for included_tool in definition.included_optional_tools:
                     included_tool = get_updated_tool_name(included_tool)
-                    if not registry.is_valid_tool_name(included_tool):
-                        raise ValueError(f"Invalid tool name '{included_tool}' provided for inclusion")
-                    if included_tool not in tool_names:
+                    if registry.check_valid_tool_name(included_tool, " (in included optional tools)") and included_tool not in tool_names:
                         tool_names.add(included_tool)
                         included_tools.append(included_tool)
                 for excluded_tool in definition.excluded_tools:
                     excluded_tool = get_updated_tool_name(excluded_tool)
-                    if not registry.is_valid_tool_name(excluded_tool):
-                        raise ValueError(f"Invalid tool name '{excluded_tool}' provided for exclusion")
+                    registry.check_valid_tool_name(excluded_tool, " (in excluded tools)")
                     if excluded_tool in tool_names:
                         tool_names.remove(excluded_tool)
                         excluded_tools.append(excluded_tool)

src/serena/resources/config/contexts/chatgpt.yml

@@ -11,8 +11,7 @@ prompt: |
   a diagram in addition to your text-based communication. Note that in the chat interface you have various rendering
   options for text, html, and mermaid diagrams, as has been explained to you in your initial instructions.
 excluded_tools: []
-included_optional_tools:
-  - switch_modes
+included_optional_tools: []
 
 tool_description_overrides:
   find_symbol: |

src/serena/resources/config/contexts/claude-code.yml

@@ -12,7 +12,6 @@ excluded_tools:
   - create_text_file
   - read_file
   - execute_shell_command
-  - prepare_for_new_conversation
   - replace_content
 
 tool_description_overrides: {}

src/serena/resources/config/contexts/codex.yml

@@ -13,7 +13,6 @@ excluded_tools:
   - create_text_file
   - read_file
   - execute_shell_command
-  - prepare_for_new_conversation
   - replace_content
 
 

src/serena/resources/config/contexts/desktop-app.yml

@@ -9,7 +9,6 @@ prompt: |
   To illustrate complex relationships, consider creating diagrams in addition to your text-based communication
   (depending on the options for text, html, mermaid diagrams, etc. that you are provided with in your initial instructions).
 excluded_tools: []
-included_optional_tools:
-  - switch_modes
+included_optional_tools: []
 
 tool_description_overrides: {}

src/serena/resources/config/contexts/ide.yml

@@ -12,7 +12,6 @@ excluded_tools:
   - create_text_file
   - read_file
   - execute_shell_command
-  - prepare_for_new_conversation
 
 tool_description_overrides: {}
 

src/serena/resources/config/prompt_templates/simple_tool_outputs.yml

@@ -34,42 +34,3 @@ prompts:
     Moreover, you should create memory files for the style and conventions and a dedicated memory file for
     what should be done when a task is completed.
     **Important**: after done with the onboarding task, remember to call the `write_memory` to save the collected information!
-
-  think_about_collected_information: |
-    Have you collected all the information you need for solving the current task? If not, can the missing information be acquired by using the available tools,
-    in particular the tools related to symbol discovery? Or do you need to ask the user for more information?
-    Think about it step by step and give a summary of the missing information and how it could be acquired.
-
-  think_about_task_adherence: |
-    Are you deviating from the task at hand? Do you need any additional information to proceed?
-    Have you loaded all relevant memory files to see whether your implementation is fully aligned with the
-    code style, conventions, and guidelines of the project? If not, adjust your implementation accordingly
-    before modifying any code into the codebase.
-    Note that it is better to stop and ask the user for clarification
-    than to perform large changes which might not be aligned with the user's intentions.
-    If you feel like the conversation is deviating too much from the original task, apologize and suggest to the user
-    how to proceed. If the conversation became too long, create a summary of the current progress and suggest to the user
-    to start a new conversation based on that summary.
-
-  think_about_whether_you_are_done: |
-    Have you already performed all the steps required by the task? Is it appropriate to run tests and linting, and if so,
-    have you done that already? Is it appropriate to adjust non-code files like documentation and config and have you done that already?
-    Should new tests be written to cover the changes?
-    Note that a task that is just about exploring the codebase does not require running tests or linting.
-    Read the corresponding memory files to see what should be done when a task is completed. 
-
-  summarize_changes: |
-    Summarize all the changes you have made to the codebase over the course of the conversation.
-    Explore the diff if needed (e.g. by using `git diff`) to ensure that you have not missed anything.
-    Explain whether and how the changes are covered by tests. Explain how to best use the new code, how to understand it,
-    which existing code it affects and interacts with. Are there any dangers (like potential breaking changes or potential new problems) 
-    that the user should be aware of? Should any new documentation be written or existing documentation updated?
-    You can use tools to explore the codebase prior to writing the summary, but don't write any new code in this step until
-    the summary is complete.
-
-  prepare_for_new_conversation: |
-    You have not yet completed the current task but we are running out of context.
-    {mode_prepare_for_new_conversation}
-    Imagine that you are handing over the task to another person who has access to the
-    same tools and memory files as you do, but has not been part of the conversation so far.
-    Write a summary that can be used in the next conversation to a memory file using the `write_memory` tool.

src/serena/resources/project.template.yml

@@ -69,40 +69,41 @@ read_only: false
 # To make sure you have the latest list of tools, and to view their descriptions, 
 # execute `uv run scripts/print_tool_overview.py`.
 #
-#  * `activate_project`: Activates a project by name.
+#  * `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.
+#  * `delete_memory`: Delete a memory file. Should only happen if a user asks for it explicitly,
+#       for example by saying that the information retrieved from a memory file is no longer correct
+#       or no longer relevant for the project.
+#  * `edit_memory`: Replaces content matching a regular expression in a memory.
 #  * `execute_shell_command`: Executes a shell command.
-#  * `find_referencing_code_snippets`: Finds code snippets in which the symbol at the given location is referenced.
-#  * `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 filtered by type).
+#  * `find_file`: Finds files in the given relative paths
+#  * `find_referencing_symbols`: Finds symbols that reference the given symbol using the language server backend
+#  * `find_symbol`: Performs a global (or local) search using the language server backend.
 #  * `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`: Gets the initial instructions for the current project.
-#     Should only be used in settings where the system prompt cannot be set,
-#     e.g. in clients you have no control over, like Claude Desktop.
+#  * `initial_instructions`: Provides instructions Serena usage (i.e. the 'Serena Instructions Manual')
+#       for clients that do not read the initial instructions when the MCP server is connected.
 #  * `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.
 #  * `list_dir`: Lists files and directories in the given directory (optionally with recursion).
-#  * `list_memories`: Lists memories in Serena's project-specific memory store.
+#  * `list_memories`: List available memories. Any memory can be read using the `read_memory` tool.
 #  * `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 the 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.
-#  * `replace_lines`: Replaces a range of lines within a file with new content.
-#  * `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.
+#  * `read_memory`: Read the content of a memory file. This tool should only be used if the information
+#       is relevant to the current task. You can infer whether the information
+#       is relevant from the memory file name.
+#       You should not read the same memory file multiple times in the same conversation.
+#  * `rename_memory`: Renames or moves a memory. Moving between project and global scope is supported
+#       (e.g., renaming "global/foo" to "bar" moves it from global to project scope).
+#  * `rename_symbol`: Renames a symbol throughout the codebase using language server refactoring capabilities.
+#       For JB, we use a separate tool.
+#  * `replace_content`: Replaces content in a file (optionally using regular expressions).
+#  * `replace_symbol_body`: Replaces the full definition of a symbol using the language server backend.
+#  * `safe_delete_symbol`:
 #  * `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.
+#  * `write_memory`: Write some information (utf-8-encoded) about this project that can be useful for future tasks to a memory in md format.
+#       The memory name should be meaningful.
 excluded_tools: []
 
 # list of tools to include that would otherwise be disabled (particularly optional tools that are disabled by default).

src/serena/tools/config_tools.py

@@ -51,27 +51,6 @@ class RemoveProjectTool(Tool, ToolMarkerDoesNotRequireActiveProject, ToolMarkerO
         return f"Successfully removed project '{project_name}' from configuration."
 
 
-class SwitchModesTool(Tool, ToolMarkerOptional):
-    """
-    Activates modes by providing a list of their names
-    """
-
-    def apply(self, modes: list[str]) -> str:
-        """
-        Activates the desired modes, like ["editing", "interactive"] or ["planning", "one-shot"]
-
-        :param modes: the names of the modes to activate
-        """
-        self.agent.set_modes(modes)
-
-        # Inform the Agent about the activated modes and the currently active tools
-        mode_instances = self.agent.get_active_modes()
-        result_str = f"Active modes: {', '.join([mode.name for mode in mode_instances])}" + "\n"
-        result_str += "\n".join([mode_instance.prompt for mode_instance in mode_instances]) + "\n"
-        result_str += f"Currently active tools: {', '.join(self.agent.get_active_tool_names())}"
-        return result_str
-
-
 class GetCurrentConfigTool(Tool):
     """
     Prints the current configuration of the agent, including the active and available projects, tools, contexts, and modes.

src/serena/tools/tools_base.py

@@ -429,6 +429,15 @@ tool_packages = ["serena.tools"]
 
 @singleton
 class ToolRegistry:
+    _deleted_tools: list[str] = [
+        "think_about_collected_information",
+        "think_about_collected_information",
+        "prepare_for_new_conversation",
+        "summarize_changes",
+        "think_about_whether_you_are_done",
+        "switch_modes",
+    ]
+
     def __init__(self) -> None:
         self._tool_dict: dict[str, RegisteredTool] = {}
         inclusion_predicate = lambda c: "apply" in c.__dict__  # include only concrete tool classes that implement apply
@@ -518,3 +527,15 @@ class ToolRegistry:
 
     def is_valid_tool_name(self, tool_name: str) -> bool:
         return tool_name in self._tool_dict
+
+    def check_valid_tool_name(self, tool_name: str, caller_context_for_logging: str = "") -> bool:
+        """Returns True if the tool name is valid, False if it is deleted, and raises ValueError if it is invalid."""
+        if self.is_deleted_tool_name(tool_name):
+            log.warning(f"Tool name is deleted: {tool_name}{caller_context_for_logging}")
+            return False
+        if not self.is_valid_tool_name(tool_name):
+            raise ValueError(f"Invalid tool name: {tool_name}{caller_context_for_logging}")
+        return True
+
+    def is_deleted_tool_name(self, tool_name: str) -> bool:
+        return tool_name in self._deleted_tools

src/serena/tools/workflow_tools.py

@@ -4,7 +4,7 @@ Tools supporting the general workflow of the agent
 
 import platform
 
-from serena.tools import Tool, ToolMarkerDoesNotRequireActiveProject, ToolMarkerOptional
+from serena.tools import Tool, ToolMarkerDoesNotRequireActiveProject
 
 
 class CheckOnboardingPerformedTool(Tool):
@@ -50,74 +50,6 @@ class OnboardingTool(Tool):
         return self.prompt_factory.create_onboarding_prompt(system=system)
 
 
-class ThinkAboutCollectedInformationTool(Tool, ToolMarkerOptional):
-    """
-    Thinking tool for pondering the completeness of collected information.
-    """
-
-    def apply(self) -> str:
-        """
-        Think about the collected information and whether it is sufficient and relevant.
-        This tool should ALWAYS be called after you have completed a non-trivial sequence of searching steps like
-        find_symbol, find_referencing_symbols, search_files_for_pattern, read_file, etc.
-        """
-        return self.prompt_factory.create_think_about_collected_information()
-
-
-class ThinkAboutTaskAdherenceTool(Tool, ToolMarkerOptional):
-    """
-    Thinking tool for determining whether the agent is still on track with the current task.
-    """
-
-    def apply(self) -> str:
-        """
-        Think about the task at hand and whether you are still on track.
-        Especially important if the conversation has been going on for a while and there
-        has been a lot of back and forth.
-
-        This tool should ALWAYS be called before you insert, replace, or delete code.
-        """
-        return self.prompt_factory.create_think_about_task_adherence()
-
-
-class ThinkAboutWhetherYouAreDoneTool(Tool, ToolMarkerOptional):
-    """
-    Thinking tool for determining whether the task is truly completed.
-    """
-
-    def apply(self) -> str:
-        """
-        Whenever you feel that you are done with what the user has asked for, it is important to call this tool.
-        """
-        return self.prompt_factory.create_think_about_whether_you_are_done()
-
-
-class SummarizeChangesTool(Tool, ToolMarkerOptional):
-    """
-    Provides instructions for summarizing the changes made to the codebase.
-    """
-
-    def apply(self) -> str:
-        """
-        Summarize the changes you have made to the codebase.
-        This tool should always be called after you have fully completed any non-trivial coding task,
-        but only after the think_about_whether_you_are_done call.
-        """
-        return self.prompt_factory.create_summarize_changes()
-
-
-class PrepareForNewConversationTool(Tool):
-    """
-    Provides instructions for preparing for a new conversation (in order to continue with the necessary context).
-    """
-
-    def apply(self) -> str:
-        """
-        Instructions for preparing for a new conversation. This tool should only be called on explicit user request.
-        """
-        return self.prompt_factory.create_prepare_for_new_conversation()
-
-
 class InitialInstructionsTool(Tool, ToolMarkerDoesNotRequireActiveProject):
     """
     Provides instructions Serena usage (i.e. the 'Serena Instructions Manual')