From 0aaeaef64cfdce1be1663f5b2e02f0c39e8aa070 Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Sun, 27 Jul 2025 15:16:57 +0200
Subject: [PATCH 1/9] Updated mcp dependency

---
 uv.lock | 130 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 65 insertions(+), 65 deletions(-)

diff --git a/uv.lock b/uv.lock
index 52fe9264..4322e294 100644
--- a/uv.lock
+++ b/uv.lock
@@ -4,7 +4,7 @@ requires-python = "==3.11.*"
 
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@@ -20,9 +20,9 @@ dependencies = [
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     { name = "typing-extensions" },
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+    { url = "https://files.pythonhosted.org/packages/34/04/b6b00383cf2f48e8e78e14eb258942fdf2a9bf0287fbf5cdd398b749193a/ruff-0.12.5-py3-none-musllinux_1_2_x86_64.whl", hash = "sha256:5a655a0a0d396f0f072faafc18ebd59adde8ca85fb848dc1b0d9f024b9c4d3bb", size = 12991537, upload-time = "2025-07-24T13:26:28.533Z" },
+    { url = "https://files.pythonhosted.org/packages/3e/b9/053d6445dc7544fb6594785056d8ece61daae7214859ada4a152ad56b6e0/ruff-0.12.5-py3-none-win32.whl", hash = "sha256:dfeb2627c459b0b78ca2bbdc38dd11cc9a0a88bf91db982058b26ce41714ffa9", size = 11751575, upload-time = "2025-07-24T13:26:30.835Z" },
+    { url = "https://files.pythonhosted.org/packages/bc/0f/ab16e8259493137598b9149734fec2e06fdeda9837e6f634f5c4e35916da/ruff-0.12.5-py3-none-win_amd64.whl", hash = "sha256:ae0d90cf5f49466c954991b9d8b953bd093c32c27608e409ae3564c63c5306a5", size = 12882273, upload-time = "2025-07-24T13:26:32.929Z" },
+    { url = "https://files.pythonhosted.org/packages/00/db/c376b0661c24cf770cb8815268190668ec1330eba8374a126ceef8c72d55/ruff-0.12.5-py3-none-win_arm64.whl", hash = "sha256:48cdbfc633de2c5c37d9f090ba3b352d1576b0015bfc3bc98eaf230275b7e805", size = 11951564, upload-time = "2025-07-24T13:26:34.994Z" },
 ]
 
 [[package]]
@@ -1250,14 +1250,14 @@ wheels = [
 
 [[package]]
 name = "sse-starlette"
-version = "2.4.1"
+version = "3.0.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/07/3e/eae74d8d33e3262bae0a7e023bb43d8bdd27980aa3557333f4632611151f/sse_starlette-2.4.1.tar.gz", hash = "sha256:7c8a800a1ca343e9165fc06bbda45c78e4c6166320707ae30b416c42da070926", size = 18635, upload-time = "2025-07-06T09:41:33.631Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/42/6f/22ed6e33f8a9e76ca0a412405f31abb844b779d52c5f96660766edcd737c/sse_starlette-3.0.2.tar.gz", hash = "sha256:ccd60b5765ebb3584d0de2d7a6e4f745672581de4f5005ab31c3a25d10b52b3a", size = 20985, upload-time = "2025-07-27T09:07:44.565Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/e4/f1/6c7eaa8187ba789a6dd6d74430307478d2a91c23a5452ab339b6fbe15a08/sse_starlette-2.4.1-py3-none-any.whl", hash = "sha256:08b77ea898ab1a13a428b2b6f73cfe6d0e607a7b4e15b9bb23e4a37b087fd39a", size = 10824, upload-time = "2025-07-06T09:41:32.321Z" },
+    { url = "https://files.pythonhosted.org/packages/ef/10/c78f463b4ef22eef8491f218f692be838282cd65480f6e423d7730dfd1fb/sse_starlette-3.0.2-py3-none-any.whl", hash = "sha256:16b7cbfddbcd4eaca11f7b586f3b8a080f1afe952c15813455b162edea619e5a", size = 11297, upload-time = "2025-07-27T09:07:43.268Z" },
 ]
 
 [[package]]
@@ -1276,15 +1276,15 @@ wheels = [
 
 [[package]]
 name = "starlette"
-version = "0.47.1"
+version = "0.47.2"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "anyio" },
     { name = "typing-extensions" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/0a/69/662169fdb92fb96ec3eaee218cf540a629d629c86d7993d9651226a6789b/starlette-0.47.1.tar.gz", hash = "sha256:aef012dd2b6be325ffa16698f9dc533614fb1cebd593a906b90dc1025529a79b", size = 2583072, upload-time = "2025-06-21T04:03:17.337Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/04/57/d062573f391d062710d4088fa1369428c38d51460ab6fedff920efef932e/starlette-0.47.2.tar.gz", hash = "sha256:6ae9aa5db235e4846decc1e7b79c4f346adf41e9777aebeb49dfd09bbd7023d8", size = 2583948, upload-time = "2025-07-20T17:31:58.522Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/82/95/38ef0cd7fa11eaba6a99b3c4f5ac948d8bc6ff199aabd327a29cc000840c/starlette-0.47.1-py3-none-any.whl", hash = "sha256:5e11c9f5c7c3f24959edbf2dffdc01bba860228acf657129467d8a7468591527", size = 72747, upload-time = "2025-06-21T04:03:15.705Z" },
+    { url = "https://files.pythonhosted.org/packages/f7/1f/b876b1f83aef204198a42dc101613fefccb32258e5428b5f9259677864b4/starlette-0.47.2-py3-none-any.whl", hash = "sha256:c5847e96134e5c5371ee9fac6fdf1a67336d5815e09eb2a01fdb57a351ef915b", size = 72984, upload-time = "2025-07-20T17:31:56.738Z" },
 ]
 
 [[package]]

From 770e3658eb35fbbb1657c3ab4a3e23f486a21baa Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Sun, 27 Jul 2025 15:17:34 +0200
Subject: [PATCH 2/9] MCP: Pass initial instructions to fastmcp constructor

---
 src/serena/mcp.py | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/serena/mcp.py b/src/serena/mcp.py
index ff8a11ba..f5f785e0 100644
--- a/src/serena/mcp.py
+++ b/src/serena/mcp.py
@@ -172,7 +172,8 @@ class SerenaMCPFactory:
         Settings.model_config = SettingsConfigDict(env_prefix="FASTMCP_")
 
         mcp_settings: Settings = Settings(lifespan=self.server_lifespan, host=host, port=port)
-        mcp = FastMCP(**mcp_settings.model_dump())
+        instructions = self._get_initial_instructions()
+        mcp = FastMCP(**mcp_settings.model_dump(), instructions=instructions)
         return mcp
 
     @asynccontextmanager
@@ -181,6 +182,10 @@ class SerenaMCPFactory:
         """Manage server startup and shutdown lifecycle."""
         yield None  # ensures MyPy understands we yield None
 
+    @abstractmethod
+    def _get_initial_instructions(self) -> str:
+        pass
+
 
 class SerenaMCPFactorySingleProcess(SerenaMCPFactory):
     """
@@ -207,6 +212,11 @@ class SerenaMCPFactorySingleProcess(SerenaMCPFactory):
         assert self.agent is not None
         yield from self.agent.get_exposed_tool_instances()
 
+    def _get_initial_instructions(self) -> str:
+        assert self.agent is not None
+        # we don't use the tool (which at the time of writing calls this method), since the tool may be disabled by the config
+        return self.agent.create_system_prompt()
+
     @asynccontextmanager
     async def server_lifespan(self, mcp_server: FastMCP) -> AsyncIterator[None]:
         self._set_mcp_tools(mcp_server)

From f30005fe4bee4854872b2ff10fe563b9a9f743f0 Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Sun, 27 Jul 2025 15:22:17 +0200
Subject: [PATCH 3/9] MCP: Updated readme on using initial instructions

---
 README.md | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/README.md b/README.md
index 788ac9b6..24abe333 100644
--- a/README.md
+++ b/README.md
@@ -354,11 +354,14 @@ For example, when using `uvx`, you would run
 claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena-mcp-server --context ide-assistant --project $(pwd)
 ```
 
-ℹ️ Serena comes with an instruction text, and Claude needs to read it to properly use Serena's tools. 
-  Once in Claude Code, you can ask to "read Serena's initial instructions" or run `/mcp__serena__initial_instructions` to load the instruction text. 
-  Do this whenever you start a new conversation and after any compacting operation to ensure Claude remains properly configured to use Serena's tools.
+ℹ️ Serena comes with an instruction text, and Claude needs to read it to properly use Serena's tools.
+  As of version `v1.0.52`, claude code reads the instructions of the MCP server, so this is handled automatically.
+  If you are using an older version, or if Claude fails to read the instructions, you can ask it explicitly
+  to "read Serena's initial instructions" or run `/mcp__serena__initial_instructions` to load the instruction text. 
+  You may have to do that whenever you start a new conversation and after any compacting operation to ensure Claude remains properly configured to use Serena's tools.
 
-ℹ️ **NEW**: an alternative to the above is adding the instructions as part of the system prompt, then you will not need to run the command above or to remember re-running it after compacting.
+ℹ️ If Claude is not automatically picking up on the instructions and running Serena's tools, and you don't want to run the command in each session,
+  an alternative to the above is adding the instructions as part of the system prompt, then you will not need to run the command above or to remember re-running it after compacting.
   This can be achieved through starting claude code with `claude --append-system-prompt $(uvx --from git+https://github.com/oraios/serena serena print-system-prompt)`. Note that this is **experimental**, Claude may not understand the instructions correctly in this way, and we haven't thoroughly tested the resulting behavior. Please report any issues you encounter.
 
 

From 3e49c83d89e29c08fbd6710a3ce4df3e342f3ffd Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Tue, 29 Jul 2025 15:55:07 +0200
Subject: [PATCH 4/9] Made initial instructions tool optional

---
 src/serena/tools/workflow_tools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/serena/tools/workflow_tools.py b/src/serena/tools/workflow_tools.py
index 6172cc33..38cc19be 100644
--- a/src/serena/tools/workflow_tools.py
+++ b/src/serena/tools/workflow_tools.py
@@ -5,7 +5,7 @@ Tools supporting the general workflow of the agent
 import json
 import platform
 
-from serena.tools import Tool, ToolMarkerDoesNotRequireActiveProject
+from serena.tools import Tool, ToolMarkerDoesNotRequireActiveProject, ToolMarkerOptional
 
 
 class CheckOnboardingPerformedTool(Tool):
@@ -122,7 +122,7 @@ class PrepareForNewConversationTool(Tool):
         return self.prompt_factory.create_prepare_for_new_conversation()
 
 
-class InitialInstructionsTool(Tool, ToolMarkerDoesNotRequireActiveProject):
+class InitialInstructionsTool(Tool, ToolMarkerDoesNotRequireActiveProject, ToolMarkerOptional):
     """
     Gets the initial instructions for the current project.
     Should only be used in settings where the system prompt cannot be set,

From 534567f11e087beed8012d968114f9560b4b8beb Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Tue, 29 Jul 2025 15:57:40 +0200
Subject: [PATCH 5/9] Excluded more tools in ide-assistant mode

Namely:
  - prepare_for_new_conversation
  - summarize_changes
  - get_current_config
---
 src/serena/resources/config/contexts/ide-assistant.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/serena/resources/config/contexts/ide-assistant.yml b/src/serena/resources/config/contexts/ide-assistant.yml
index d40cb860..2a6c9e2c 100644
--- a/src/serena/resources/config/contexts/ide-assistant.yml
+++ b/src/serena/resources/config/contexts/ide-assistant.yml
@@ -22,4 +22,7 @@ excluded_tools:
   - delete_lines
   - replace_lines
   - insert_at_line
-  - execute_shell_command
\ No newline at end of file
+  - execute_shell_command
+  - prepare_for_new_conversation
+  - summarize_changes
+  - get_current_config

From d624c1c0b9241a549f50e1c202860932dbfe040d Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Wed, 30 Jul 2025 12:07:30 +0200
Subject: [PATCH 6/9] Allow passing a list of dirs as prompts_dir, the tail of
 the list serving as fallbacks

---
 src/interprompt/multilang_prompt.py | 96 +++++++++++++++++++++++++----
 src/interprompt/prompt_factory.py   |  6 +-
 2 files changed, 88 insertions(+), 14 deletions(-)

diff --git a/src/interprompt/multilang_prompt.py b/src/interprompt/multilang_prompt.py
index 55777344..e7322efb 100644
--- a/src/interprompt/multilang_prompt.py
+++ b/src/interprompt/multilang_prompt.py
@@ -1,7 +1,7 @@
 import logging
 import os
 from enum import Enum
-from typing import Any, Generic, TypeVar
+from typing import Any, Generic, Literal, TypeVar
 
 import yaml
 from sensai.util.string import ToStringMixin
@@ -92,6 +92,9 @@ class _MultiLangContainer(Generic[T], ToStringMixin):
             raise KeyError(f"Item for language '{lang_code}' already registered for name '{self.name}'")
         self._lang2item[lang_code] = item
 
+    def has_item(self, lang_code: str = DEFAULT_LANG_CODE) -> bool:
+        return lang_code in self._lang2item
+
     def get_item(self, lang: str = DEFAULT_LANG_CODE, fallback_mode: LanguageFallbackMode = LanguageFallbackMode.EXCEPTION) -> T:
         """
         Gets the item for the given language.
@@ -183,6 +186,9 @@ class MultiLangPromptTemplate(ParameterizedTemplateInterface):
         prompt_template = self.get_prompt_template(lang_code, fallback_mode)
         return prompt_template.render(**params)
 
+    def has_item(self, lang_code: str = DEFAULT_LANG_CODE) -> bool:
+        return self._prompts_container.has_item(lang_code)
+
 
 class MultiLangPromptList(_MultiLangContainer[PromptList]):
     pass
@@ -212,44 +218,96 @@ class MultiLangPromptCollection:
     The prompt names must be unique (for the same language) within the collection.
     """
 
-    def __init__(self, prompts_dir: str, fallback_mode: LanguageFallbackMode = LanguageFallbackMode.EXCEPTION) -> None:
+    def __init__(self, prompts_dir: str | list[str], fallback_mode: LanguageFallbackMode = LanguageFallbackMode.EXCEPTION) -> None:
         """
-        :param prompts_dir: the directory containing the prompt templates and prompt lists
+        :param prompts_dir: the directory containing the prompt templates and prompt lists.
+            If a list is provided, will look for prompt templates in the dirs from left to right
+            (first one containing the desired template wins).
         :param fallback_mode: the fallback mode to use when a prompt template or prompt list is not found for the requested language.
             May be reset after initialization.
         """
         self._multi_lang_prompt_templates: dict[str, MultiLangPromptTemplate] = {}
         self._multi_lang_prompt_lists: dict[str, MultiLangPromptList] = {}
-        self._load_from_disc(prompts_dir)
+        if isinstance(prompts_dir, str):
+            prompts_dir = [prompts_dir]
+
+        # Add prompts from multiple directories, prioritizing names from the left.
+        # If name collisions appear in the first directory, an error is raised (so the first directory should have no
+        # internal collisions, this helps in avoiding errors)
+        # For all following directories, on a collision the new value will be ignored.
+        # This also means that for the following directories, there is no error check on collisions internal to them.
+        # We assume that they are correct (i.e., they have no internal collisions).
+        first_prompts_dir, fallback_prompt_dirs = prompts_dir[0], prompts_dir[1:]
+        self._load_from_disc(first_prompts_dir, on_name_collision="raise")
+        for fallback_prompt_dir in fallback_prompt_dirs:
+            # already loaded prompts have priority
+            self._load_from_disc(fallback_prompt_dir, on_name_collision="skip")
+
         self.fallback_mode = fallback_mode
 
-    def _add_prompt_template(self, name: str, template_str: str, lang_code: str = DEFAULT_LANG_CODE) -> None:
+    def _add_prompt_template(
+        self,
+        name: str,
+        template_str: str,
+        lang_code: str = DEFAULT_LANG_CODE,
+        on_name_collision: Literal["skip", "overwrite", "raise"] = "raise",
+    ) -> None:
         """
         :param name: name of the prompt template
         :param template_str: the Jinja template string
         :param lang_code: the language code for which to add the prompt template.
+        :param on_name_collision: how to deal with name/lang_code collisions
         """
+        allow_overwrite = False
         prompt_template = PromptTemplate(name, template_str)
         mlpt = self._multi_lang_prompt_templates.get(name)
         if mlpt is None:
             mlpt = MultiLangPromptTemplate(name)
             self._multi_lang_prompt_templates[name] = mlpt
-        mlpt.add_prompt_template(prompt_template, lang_code=lang_code)
+        if mlpt.has_item(lang_code):
+            if on_name_collision == "raise":
+                raise KeyError(f"Prompt '{name}' for {lang_code} already exists!")
+            if on_name_collision == "skip":
+                log.debug(f"Skipping prompt '{name}' since it already exists.")
+                return
+            elif on_name_collision == "overwrite":
+                allow_overwrite = True
+        mlpt.add_prompt_template(prompt_template, lang_code=lang_code, allow_overwrite=allow_overwrite)
 
-    def _add_prompt_list(self, name: str, prompt_list: list[str], lang_code: str = DEFAULT_LANG_CODE) -> None:
+    def _add_prompt_list(
+        self,
+        name: str,
+        prompt_list: list[str],
+        lang_code: str = DEFAULT_LANG_CODE,
+        on_name_collision: Literal["skip", "overwrite", "raise"] = "raise",
+    ) -> None:
         """
         :param name: name of the prompt list
         :param prompt_list: a list of prompts
         :param lang_code: the language code for which to add the prompt list.
+        :param on_name_collision: how to deal with name/lang_code collisions
         """
+        allow_overwrite = False
         multilang_prompt_list = self._multi_lang_prompt_lists.get(name)
         if multilang_prompt_list is None:
             multilang_prompt_list = MultiLangPromptList(name)
             self._multi_lang_prompt_lists[name] = multilang_prompt_list
-        multilang_prompt_list.add_item(PromptList(prompt_list), lang_code=lang_code)
+        if multilang_prompt_list.has_item(lang_code):
+            if on_name_collision == "raise":
+                raise KeyError(f"Prompt '{name}' for {lang_code} already exists!")
+            if on_name_collision == "skip":
+                log.debug(f"Skipping prompt '{name}' since it already exists.")
+                return
+            elif on_name_collision == "overwrite":
+                allow_overwrite = True
+        multilang_prompt_list.add_item(PromptList(prompt_list), lang_code=lang_code, allow_overwrite=allow_overwrite)
 
-    def _load_from_disc(self, prompts_dir: str) -> None:
-        """Loads all prompt templates and prompt lists from yaml files in the given directory."""
+    def _load_from_disc(self, prompts_dir: str, on_name_collision: Literal["skip", "overwrite", "raise"] = "raise") -> None:
+        """Loads all prompt templates and prompt lists from yaml files in the given directory.
+
+        :param prompts_dir:
+        :param on_name_collision: how to deal with name/lang_code collisions
+        """
         for fn in os.listdir(prompts_dir):
             if not fn.endswith((".yml", ".yaml")):
                 log.debug(f"Skipping non-YAML file: {fn}")
@@ -266,9 +324,11 @@ class MultiLangPromptCollection:
             # add the data to the collection
             for prompt_name, prompt_template_or_list in prompts_data.items():
                 if isinstance(prompt_template_or_list, list):
-                    self._add_prompt_list(prompt_name, prompt_template_or_list, lang_code=lang_code)
+                    self._add_prompt_list(prompt_name, prompt_template_or_list, lang_code=lang_code, on_name_collision=on_name_collision)
                 elif isinstance(prompt_template_or_list, str):
-                    self._add_prompt_template(prompt_name, prompt_template_or_list, lang_code=lang_code)
+                    self._add_prompt_template(
+                        prompt_name, prompt_template_or_list, lang_code=lang_code, on_name_collision=on_name_collision
+                    )
                 else:
                     raise ValueError(
                         f"Invalid prompt type for {prompt_name} in file {path} (should be str or list): {prompt_template_or_list}"
@@ -306,6 +366,18 @@ class MultiLangPromptCollection:
         """The PromptList object for the given prompt name and language code."""
         return self.get_multilang_prompt_list(prompt_name).get_item(lang_code)
 
+    def _has_prompt_list(self, prompt_name: str, lang_code: str = DEFAULT_LANG_CODE) -> bool:
+        multi_lang_prompt_list = self._multi_lang_prompt_lists.get(prompt_name)
+        if multi_lang_prompt_list is None:
+            return False
+        return multi_lang_prompt_list.has_item(lang_code)
+
+    def _has_prompt_template(self, prompt_name: str, lang_code: str = DEFAULT_LANG_CODE) -> bool:
+        multi_lang_prompt_template = self._multi_lang_prompt_templates.get(prompt_name)
+        if multi_lang_prompt_template is None:
+            return False
+        return multi_lang_prompt_template.has_item(lang_code)
+
     def render_prompt_template(
         self,
         prompt_name: str,
diff --git a/src/interprompt/prompt_factory.py b/src/interprompt/prompt_factory.py
index 3aa9da08..1769e7f2 100644
--- a/src/interprompt/prompt_factory.py
+++ b/src/interprompt/prompt_factory.py
@@ -10,9 +10,11 @@ log = logging.getLogger(__name__)
 class PromptFactoryBase:
     """Base class for auto-generated prompt factory classes."""
 
-    def __init__(self, prompts_dir: str, lang_code: str = DEFAULT_LANG_CODE, fallback_mode=LanguageFallbackMode.EXCEPTION):
+    def __init__(self, prompts_dir: str | list[str], lang_code: str = DEFAULT_LANG_CODE, fallback_mode=LanguageFallbackMode.EXCEPTION):
         """
-        :param prompts_dir: the directory containing the prompt templates and prompt lists
+        :param prompts_dir: the directory containing the prompt templates and prompt lists.
+            If a list is provided, will look for prompt templates in the dirs from left to right
+            (first one containing the desired template wins).
         :param lang_code: the language code to use for retrieving the prompt templates and prompt lists.
             Leave as `default` for single-language use cases.
         :param fallback_mode: the fallback mode to use when a prompt template or prompt list is not found for the requested language.

From caa2c545e4c8870421e47c87e1b698f4c6fbc5d3 Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Wed, 30 Jul 2025 12:10:15 +0200
Subject: [PATCH 7/9] New feature: allow users to override prompts. Extended
 CLI for that

---
 scripts/gen_prompt_factory.py |  4 +-
 src/serena/cli.py             | 91 ++++++++++++++++++++++++++++++++++-
 src/serena/constants.py       |  3 +-
 src/serena/prompt_factory.py  |  7 ++-
 4 files changed, 99 insertions(+), 6 deletions(-)

diff --git a/scripts/gen_prompt_factory.py b/scripts/gen_prompt_factory.py
index 4b1354fd..4877d4d1 100644
--- a/scripts/gen_prompt_factory.py
+++ b/scripts/gen_prompt_factory.py
@@ -7,14 +7,14 @@ from pathlib import Path
 from sensai.util import logging
 
 from interprompt import autogenerate_prompt_factory_module
-from serena.constants import PROMPT_TEMPLATES_DIR, REPO_ROOT
+from serena.constants import PROMPT_TEMPLATES_DIR_INTERNAL, REPO_ROOT
 
 log = logging.getLogger(__name__)
 
 
 def main():
     autogenerate_prompt_factory_module(
-        prompts_dir=PROMPT_TEMPLATES_DIR,
+        prompts_dir=PROMPT_TEMPLATES_DIR_INTERNAL,
         target_module_path=str(Path(REPO_ROOT) / "src" / "serena" / "generated" / "generated_prompt_factory.py"),
     )
 
diff --git a/src/serena/cli.py b/src/serena/cli.py
index deb3b6e6..6b46a8e8 100644
--- a/src/serena/cli.py
+++ b/src/serena/cli.py
@@ -1,3 +1,4 @@
+import glob
 import os
 import shutil
 import subprocess
@@ -16,6 +17,8 @@ from serena.config.serena_config import ProjectConfig, SerenaConfig, SerenaPaths
 from serena.constants import (
     DEFAULT_CONTEXT,
     DEFAULT_MODES,
+    PROMPT_TEMPLATES_DIR_IN_USER_HOME,
+    PROMPT_TEMPLATES_DIR_INTERNAL,
     SERENA_LOG_FORMAT,
     SERENA_MANAGED_DIR_IN_HOME,
     SERENAS_OWN_CONTEXT_YAMLS_DIR,
@@ -476,12 +479,98 @@ class ToolCommands(AutoRegisteringGroup):
             ToolRegistry().print_tool_overview()
 
 
+class PromptCommands(AutoRegisteringGroup):
+    def __init__(self) -> None:
+        super().__init__(name="prompts", help="Commands related to Serena's prompts that are outside of contexts and modes.")
+
+    @staticmethod
+    def _get_user_prompt_yaml_path(prompt_yaml_name: str) -> str:
+        os.makedirs(PROMPT_TEMPLATES_DIR_IN_USER_HOME, exist_ok=True)
+        return os.path.join(PROMPT_TEMPLATES_DIR_IN_USER_HOME, prompt_yaml_name)
+
+    @staticmethod
+    @click.command("list", help="Lists yamls that are used for defining prompts.")
+    def list() -> None:
+        serena_prompt_yaml_names = [os.path.basename(f) for f in glob.glob(PROMPT_TEMPLATES_DIR_INTERNAL + "/*.yml")]
+        for prompt_yaml_name in serena_prompt_yaml_names:
+            user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
+            if os.path.exists(user_prompt_yaml_path):
+                click.echo(f"{user_prompt_yaml_path} merged with default prompts in {prompt_yaml_name}")
+            else:
+                click.echo(prompt_yaml_name)
+
+    @staticmethod
+    @click.command("create-override", help="Create an override of an internal prompts yaml for customizing Serena's prompts")
+    @click.argument("prompt_yaml_name")
+    def create_override(prompt_yaml_name: str) -> None:
+        """
+        :param prompt_yaml_name: The yaml name of the prompt you want to override. Call the `list` command for discovering valid prompt yaml names.
+        :return:
+        """
+        # for convenience, we can pass names without .yml
+        if not prompt_yaml_name.endswith(".yml"):
+            prompt_yaml_name = prompt_yaml_name + ".yml"
+        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
+        if os.path.exists(user_prompt_yaml_path):
+            raise FileExistsError(f"{user_prompt_yaml_path} already exists.")
+        serena_prompt_yaml_path = os.path.join(PROMPT_TEMPLATES_DIR_INTERNAL, prompt_yaml_name)
+        shutil.copyfile(serena_prompt_yaml_path, user_prompt_yaml_path)
+        _open_in_editor(user_prompt_yaml_path)
+
+    @staticmethod
+    @click.command("edit-override", help="Edit an existing prompt override file")
+    @click.argument("prompt_yaml_name")
+    def edit_override(prompt_yaml_name: str) -> None:
+        """
+        :param prompt_yaml_name: The yaml name of the prompt override to edit.
+        :return:
+        """
+        # for convenience, we can pass names without .yml
+        if not prompt_yaml_name.endswith(".yml"):
+            prompt_yaml_name = prompt_yaml_name + ".yml"
+        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
+        if not os.path.exists(user_prompt_yaml_path):
+            click.echo(f"Override file '{prompt_yaml_name}' not found. Create it with: prompts create-override {prompt_yaml_name}")
+            return
+        _open_in_editor(user_prompt_yaml_path)
+
+    @staticmethod
+    @click.command("list-overrides", help="List existing prompt override files")
+    def list_overrides() -> None:
+        os.makedirs(PROMPT_TEMPLATES_DIR_IN_USER_HOME, exist_ok=True)
+        serena_prompt_yaml_names = [os.path.basename(f) for f in glob.glob(PROMPT_TEMPLATES_DIR_INTERNAL + "/*.yml")]
+        override_files = glob.glob(os.path.join(PROMPT_TEMPLATES_DIR_IN_USER_HOME, "*.yml"))
+        for file_path in override_files:
+            if os.path.basename(file_path) in serena_prompt_yaml_names:
+                click.echo(file_path)
+
+    @staticmethod
+    @click.command("delete-override", help="Delete a prompt override file")
+    @click.argument("prompt_yaml_name")
+    def delete_override(prompt_yaml_name: str) -> None:
+        """
+
+        :param prompt_yaml_name:  The yaml name of the prompt override to delete."
+        :return:
+        """
+        # for convenience, we can pass names without .yml
+        if not prompt_yaml_name.endswith(".yml"):
+            prompt_yaml_name = prompt_yaml_name + ".yml"
+        user_prompt_yaml_path = PromptCommands._get_user_prompt_yaml_path(prompt_yaml_name)
+        if not os.path.exists(user_prompt_yaml_path):
+            click.echo(f"Override file '{prompt_yaml_name}' not found.")
+            return
+        os.remove(user_prompt_yaml_path)
+        click.echo(f"Deleted override file '{prompt_yaml_name}'.")
+
+
 # Expose groups so we can reference them in pyproject.toml
 mode = ModeCommands()
 context = ContextCommands()
 project = ProjectCommands()
 config = SerenaConfigCommands()
 tools = ToolCommands()
+prompts = PromptCommands()
 
 # Expose toplevel commands for the same reason
 top_level = TopLevelCommands()
@@ -489,7 +578,7 @@ start_mcp_server = top_level.start_mcp_server
 index_project = project.index_deprecated
 
 # needed for the help script to work - register all subcommands to the top-level group
-for subgroup in (mode, context, project, config, tools):
+for subgroup in (mode, context, project, config, tools, prompts):
     top_level.add_command(subgroup)
 
 
diff --git a/src/serena/constants.py b/src/serena/constants.py
index 9b0dd43f..d25f5c45 100644
--- a/src/serena/constants.py
+++ b/src/serena/constants.py
@@ -10,7 +10,8 @@ SERENA_MANAGED_DIR_IN_HOME = str(_serena_in_home_managed_dir)
 
 # TODO: Path-related constants should be moved to SerenaPaths; don't add further constants here.
 REPO_ROOT = str(_repo_root_path)
-PROMPT_TEMPLATES_DIR = str(_serena_pkg_path / "resources" / "config" / "prompt_templates")
+PROMPT_TEMPLATES_DIR_INTERNAL = str(_serena_pkg_path / "resources" / "config" / "prompt_templates")
+PROMPT_TEMPLATES_DIR_IN_USER_HOME = str(_serena_in_home_managed_dir / "prompt_templates")
 SERENAS_OWN_CONTEXT_YAMLS_DIR = str(_serena_pkg_path / "resources" / "config" / "contexts")
 """The contexts that are shipped with the Serena package, i.e. the default contexts."""
 USER_CONTEXT_YAMLS_DIR = str(_serena_in_home_managed_dir / "contexts")
diff --git a/src/serena/prompt_factory.py b/src/serena/prompt_factory.py
index f4f02ca7..40f51e7a 100644
--- a/src/serena/prompt_factory.py
+++ b/src/serena/prompt_factory.py
@@ -1,4 +1,6 @@
-from serena.constants import PROMPT_TEMPLATES_DIR
+import os
+
+from serena.constants import PROMPT_TEMPLATES_DIR_IN_USER_HOME, PROMPT_TEMPLATES_DIR_INTERNAL
 from serena.generated.generated_prompt_factory import PromptFactory
 
 
@@ -8,4 +10,5 @@ class SerenaPromptFactory(PromptFactory):
     """
 
     def __init__(self) -> None:
-        super().__init__(PROMPT_TEMPLATES_DIR)
+        os.makedirs(PROMPT_TEMPLATES_DIR_IN_USER_HOME, exist_ok=True)
+        super().__init__(prompts_dir=[PROMPT_TEMPLATES_DIR_IN_USER_HOME, PROMPT_TEMPLATES_DIR_INTERNAL])

From d26dc3536af36d90c2156630326ce73ee89cbe96 Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Thu, 31 Jul 2025 11:52:51 +0200
Subject: [PATCH 8/9] Readme: more info on CLI, initial instructions, and
 included_optional_tools

---
 README.md | 109 ++++++++++++++++++++++++++----------------------------
 1 file changed, 53 insertions(+), 56 deletions(-)

diff --git a/README.md b/README.md
index 24abe333..cfe3aa44 100644
--- a/README.md
+++ b/README.md
@@ -202,38 +202,27 @@ This and other settings can be adjusted in the [configuration](#configuration) a
    git clone https://github.com/oraios/serena
    cd serena
    ```
-2. Optionally create the configuration file in your home directory, i.e.
-
-      * `~/.serena/serena_config.yml` on Linux and macOS, or
-      * `%USERPROFILE%\.serena\serena_config.yml` on Windows.  
-
-   by copying the template and then adjusting it according to your needs:   
+2. Optionally edit the configuration file in your home directory with 
    ```shell
-   mkdir ~/.serena
-   cp src/serena/resources/serena_config.template.yml ~/.serena/serena_config.yml
+   uv run serena config edit
    ```
    If you just want the default config, you can skip this part, and a config file will be created when you first run Serena.
 3. Run the server with `uv`:
    ```shell
-   uv run serena-mcp-server
+   uv run serena start-mcp-server
    ```
-   When running from outside the serena installation directory, be sure to pass it, i.e. use
+   When running from outside the serena installation directory, be sure to pass it, i.e., use
    ```shell
-    uv run --directory /abs/path/to/serena serena-mcp-server
+    uv run --directory /abs/path/to/serena serena start-mcp-server
     ```
 
 ##### Using uvx
 
 `uvx` can be used to run the latest version of Serena directly from the repository, without an explicit local installation.
 
-* Windows:
-  ```shell
-  uvx --from git+https://github.com/oraios/serena serena-mcp-server.exe
-  ```
-* Other operating systems:
-  ```shell
-  uvx --from git+https://github.com/oraios/serena serena-mcp-server
-  ```
+```shell
+uvx --from git+https://github.com/oraios/serena serena start-mcp-server
+```
 
 ##### Using Docker (Experimental)
 
@@ -243,7 +232,7 @@ You can run the Serena MCP server directly via docker as follows,
 assuming that the projects you want to work on are all located in `/path/to/your/projects`:
 
 ```shell
-docker run --rm -i --network host -v /path/to/your/projects:/workspaces/projects ghcr.io/oraios/serena:latest serena-mcp-server --transport stdio
+docker run --rm -i --network host -v /path/to/your/projects:/workspaces/projects ghcr.io/oraios/serena:latest serena start-mcp-server --transport stdio
 ```
 
 Replace `/path/to/your/projects` with the absolute path to your projects directory. The Docker approach provides:
@@ -263,12 +252,12 @@ therefore needs to be configured with a launch command.
 When using instead the SSE mode, which uses HTTP-based communication, you control the server lifecycle yourself,
 i.e. you start the server and provide the client with the URL to connect to it.
 
-Simply provide `serena-mcp-server` with the `--transport sse` option and optionally provide the port.
+Simply provide `start-mcp-server` with the `--transport sse` option and optionally provide the port.
 For example, to run the Serena MCP server in SSE mode on port 9121 using a local installation,
 you would run this command from the Serena directory, 
 
 ```shell
-uv run serena-mcp-server --transport sse --port 9121
+uv run serena start-mcp-server --transport sse --port 9121
 ```
 
 and then configure your client to connect to `http://localhost:9121/sse`.
@@ -289,12 +278,22 @@ Serena's behavior (active tools and prompts as well as logging configuration, et
 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`.
    If you do not explicitly create the file, it will be auto-generated when you first run Serena.
-2. In the arguments passed to the `serena-mcp-server` in your client's config (see below), 
+   You can edit it directly or use
+   ```shell
+   uvx --from git+https://github.com/oraios/serena serena config edit
+   ```
+   (or use the `--directory` command version).
+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.
+   that project is activated. This file will be autogenerated when you first use Serena on that project, but you can also
+   generate it explicitly with
+   ```shell
+   uvx --from git+https://github.com/oraios/serena serena project generate-yml
+   ```
+   (or use the `--directory` command version).
 4. Through the currently active set of [modes](#modes).
 
 
@@ -323,20 +322,17 @@ project, the file `.serena/project.yml` will be generated. You can adjust the la
 same name.
 
 If you are mostly working with the same project, you can also configure to always activate a project at startup
-by passing `--project <path_or_name>` to the `serena-mcp-server` command in your client's MCP config.
+by passing `--project <path_or_name>` to the `start-mcp-server` command in your client's MCP config.
 
 ℹ️ For larger projects, we recommend that you index your project to accelerate Serena's tools; otherwise the first
 tool application may be very slow.
-To do so, run one of these commands the project directory or pass the path to the project as an argument:
+To do so, run this from the project directory (or pass the path to the project as an argument):
 
-* When using a local installation:
-  ```shell
-  uv run --directory /abs/path/to/serena index-project
-  ```
-* When using uvx:
-  ```shell
-  uvx --from git+https://github.com/oraios/serena index-project
-  ```
+```shell
+uvx --from git+https://github.com/oraios/serena serena project index
+```
+
+(or use the `--directory` command version).
 
 ### Claude Code
 
@@ -351,18 +347,16 @@ claude mcp add serena -- <serena-mcp-server> --context ide-assistant --project $
 where `<serena-mcp-server>` is your way of [running the Serena MCP server](#running-the-serena-mcp-server).
 For example, when using `uvx`, you would run
 ```shell
-claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena-mcp-server --context ide-assistant --project $(pwd)
+claude mcp add serena -- uvx --from git+https://github.com/oraios/serena serena start-mcp-server --context ide-assistant --project $(pwd)
 ```
 
 ℹ️ Serena comes with an instruction text, and Claude needs to read it to properly use Serena's tools.
-  As of version `v1.0.52`, claude code reads the instructions of the MCP server, so this is handled automatically.
+  As of version `v1.0.52`, claude code reads the instructions of the MCP server, so this **is handled automatically**.
   If you are using an older version, or if Claude fails to read the instructions, you can ask it explicitly
-  to "read Serena's initial instructions" or run `/mcp__serena__initial_instructions` to load the instruction text. 
-  You may have to do that whenever you start a new conversation and after any compacting operation to ensure Claude remains properly configured to use Serena's tools.
-
-ℹ️ If Claude is not automatically picking up on the instructions and running Serena's tools, and you don't want to run the command in each session,
-  an alternative to the above is adding the instructions as part of the system prompt, then you will not need to run the command above or to remember re-running it after compacting.
-  This can be achieved through starting claude code with `claude --append-system-prompt $(uvx --from git+https://github.com/oraios/serena serena print-system-prompt)`. Note that this is **experimental**, Claude may not understand the instructions correctly in this way, and we haven't thoroughly tested the resulting behavior. Please report any issues you encounter.
+  to "read Serena's initial instructions" or run `/mcp__serena__initial_instructions` to load the instruction text.
+  If you want to make use of that, you will have to enable the corresponding tool explicitly by adding `initial_instructions` to the `included_optional_tools`
+  in your config.
+  Note that you may have to make Claude read the instructions you start a new conversation and after any compacting operation to ensure Claude remains properly configured to use Serena's tools.
 
 
 ### Claude Desktop
@@ -377,7 +371,7 @@ Add the `serena` MCP server configuration, using a [run command](#running-the-se
        "mcpServers": {
            "serena": {
                "command": "/abs/path/to/uv",
-               "args": ["run", "--directory", "/abs/path/to/serena", "serena-mcp-server"]
+               "args": ["run", "--directory", "/abs/path/to/serena", "serena", "start-mcp-server"]
            }
        }
    }
@@ -388,7 +382,7 @@ Add the `serena` MCP server configuration, using a [run command](#running-the-se
        "mcpServers": {
            "serena": {
                "command": "/abs/path/to/uvx",
-               "args": ["--from", "git+https://github.com/oraios/serena", "serena-mcp-server"]
+               "args": ["--from", "git+https://github.com/oraios/serena", "serena", "start-mcp-server"]
            }
        }
   }
@@ -399,7 +393,7 @@ Add the `serena` MCP server configuration, using a [run command](#running-the-se
        "mcpServers": {
            "serena": {
                "command": "docker",
-               "args": ["run", "--rm", "-i", "--network", "host", "-v", "/path/to/your/projects:/workspaces/projects", "ghcr.io/oraios/serena:latest", "serena-mcp-server", "--transport", "stdio"]
+               "args": ["run", "--rm", "-i", "--network", "host", "-v", "/path/to/your/projects:/workspaces/projects", "ghcr.io/oraios/serena:latest", "serena", "start-mcp-server", "--transport", "stdio"]
            }
        }
    }
@@ -581,14 +575,20 @@ When launching Serena, specify modes using `--mode <mode-name>`; multiple modes
 #### Customization
 
 You can create your own contexts and modes to precisely tailor Serena to your needs in two ways:
-*  **Adding to Serena's configuration directory**: Create new `.yml` files in the `config/contexts/` or `config/modes/` directories within your local Serena repository. These custom contexts/modes will be automatically registered and available for use by their name (filename without the `.yml` extension). They will also appear in listings of available contexts/modes.
-*  **Using external YAML files**: When starting Serena, you can provide an absolute path to a custom `.yml` file for a context or mode.
+*   You can use Serena's CLI to manage modes and contexts. Check out
+    ```shell
+    uvx --from git+https://github.com/oraios/serena serena mode --help
+    uvx --from git+https://github.com/oraios/serena serena context --help
+    ```
+    *NOTE*: Custom contexts/modes are simply YAML files in `<home>/.serena`, they are automatically registered and available for use by their name (filename without the `.yml` extension). If you don't want to use Serena's CLI, you can create and manage them in any way you see fit.
+*  **Using external YAML files**: When starting Serena, you can also provide an absolute path to a custom `.yml` file for a context or mode.
 
 A context or mode YAML file typically defines:
 *   `name`: (Optional if filename is used) The name of the context/mode.
 *   `prompt`: A string that will be incorporated into Serena's system prompt.
-*   `description`: (Optional) A brief description.
+*   `description`: (Optional) A brief description, not passed to the LLM.
 *   `excluded_tools`: A list of tool names (strings) to disable when this context/mode is active.
+*   `included_optional_tools`: A list of tool names that are disabled by default and have to be explicitly enabled by the user.
 
 This customization allows for deep integration and adaptation of Serena to specific project requirements or personal preferences.
 
@@ -741,11 +741,10 @@ subscriptions.
 
 ### Subscription-Based Coding Agents
 
-The most prominent subscription-based coding agents are parts of IDEs like
+Many prominent subscription-based coding agents are parts of IDEs like
 Windsurf, Cursor and VSCode.
 Serena's functionality is similar to Cursor's Agent, Windsurf's Cascade or
-VSCode's
-upcoming [agent mode](https://code.visualstudio.com/blogs/2025/02/24/introducing-copilot-agent-mode).
+VSCode's agent mode.
 
 Serena has the advantage of not requiring a subscription.
 A potential disadvantage is that it
@@ -753,7 +752,7 @@ is not directly integrated into an IDE, so the inspection of newly written code
 is not as seamless.
 
 More technical differences are:
-* Serena is not bound to a specific IDE.
+* Serena is not bound to a specific IDE or CLI.
   Serena's MCP server can be used with any MCP client (including some IDEs),
   and the Agno-based agent provides additional ways of applying its functionality.
 * Serena is not bound to a specific large language model or API.
@@ -829,7 +828,7 @@ For details on contributing, see [here](/CONTRIBUTING.md).
 
 ## Full List of Tools
 
-Here is the full list of Serena's tools with a short description (output of `uv run serena-list-tools`):
+Here is the full list of Serena's tools with a short description (output of `uv run serena tools list`):
 
  * `activate_project`: Activates a project by name.
  * `check_onboarding_performed`: Checks whether project onboarding was already performed.
@@ -843,9 +842,7 @@ Here is the full list of Serena's tools with a short description (output of `uv
  * `get_active_project`: Gets the name of the currently active project (if any) and lists existing projects
  * `get_current_config`: Prints the current configuration of the agent, including the active modes, tools, and context.
  * `get_symbols_overview`: Gets an overview of the top-level symbols defined in a given file or directory.
- * `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`: Gets the initial instructions for the current project. Disabled by default, has to be enabled explicitly by using `included_optional_tools`
  * `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.

From c69e30a7bc50338bd4a3af936a3f788969e1b573 Mon Sep 17 00:00:00 2001
From: MischaPanch <mischa.panch@gmail.com>
Date: Thu, 31 Jul 2025 11:57:11 +0200
Subject: [PATCH 9/9] Readme: moved uvx install option above the local
 installation option [ci skip]

---
 README.md | 20 +++++++++++---------
 1 file changed, 11 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index cfe3aa44..1b6777cb 100644
--- a/README.md
+++ b/README.md
@@ -195,6 +195,16 @@ Note that no matter how you run the MCP server, Serena will, by default, start a
 MCP server (since many clients fail to clean up processes correctly).
 This and other settings can be adjusted in the [configuration](#configuration) and/or by providing [command-line arguments](#command-line-arguments).
 
+##### Using uvx
+
+`uvx` can be used to run the latest version of Serena directly from the repository, without an explicit local installation.
+
+```shell
+uvx --from git+https://github.com/oraios/serena serena start-mcp-server
+```
+
+Explore the CLI to see some of the customization options that serena provides (more info on them below).
+
 ###### Local Installation
 
 1. Clone the repository and change into it.
@@ -214,15 +224,7 @@ This and other settings can be adjusted in the [configuration](#configuration) a
    When running from outside the serena installation directory, be sure to pass it, i.e., use
    ```shell
     uv run --directory /abs/path/to/serena serena start-mcp-server
-    ```
-
-##### Using uvx
-
-`uvx` can be used to run the latest version of Serena directly from the repository, without an explicit local installation.
-
-```shell
-uvx --from git+https://github.com/oraios/serena serena start-mcp-server
-```
+   ```
 
 ##### Using Docker (Experimental)