From be29beaf38d9b311de7ec214f550ef70cf45efdf Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 17:03:26 +0200
Subject: [PATCH 1/9] LS: possibility to include file symbols in
 find_referencing_symbols

Some minor fixes and deduplication. Adjusted tests to only use relative paths.
---
 src/multilspy/language_server.py        | 104 +++++++++++++++++++-----
 test/multilspy/test_basic.py            |  11 +--
 test/multilspy/test_symbol_retrieval.py |  97 +++++++++++++---------
 3 files changed, 145 insertions(+), 67 deletions(-)

diff --git a/src/multilspy/language_server.py b/src/multilspy/language_server.py
index 3a7b3ae5..e320d7f5 100644
--- a/src/multilspy/language_server.py
+++ b/src/multilspy/language_server.py
@@ -6,38 +6,37 @@ The details of Language Specific configuration are not exposed to the user.
 """
 
 import asyncio
-from collections import defaultdict
-from copy import copy
 import dataclasses
-from fnmatch import fnmatch
 import hashlib
 import json
-import pickle
 import logging
 import os
 import pathlib
+import pickle
 import re
 import threading
+from collections import defaultdict
 from contextlib import asynccontextmanager, contextmanager
+from copy import copy
+from fnmatch import fnmatch
+from pathlib import Path, PurePath
+from typing import AsyncIterator, Dict, Iterator, List, Optional, Tuple, Union, cast
 
-from serena.text_utils import MatchedConsecutiveLines, LineType, TextLine, search_text
-from .lsp_protocol_handler.lsp_constants import LSPConstants
-from  .lsp_protocol_handler import lsp_types as LSPTypes
-
+from serena.text_utils import LineType, MatchedConsecutiveLines, TextLine, search_text
 from . import multilspy_types
-from .multilspy_logger import MultilspyLogger
+from .lsp_protocol_handler import lsp_types as LSPTypes
+from .lsp_protocol_handler.lsp_constants import LSPConstants
+from .lsp_protocol_handler.lsp_types import SymbolKind
 from .lsp_protocol_handler.server import (
     LanguageServerHandler,
     ProcessLaunchInfo,
 )
-from .multilspy_config import MultilspyConfig, Language
+from .multilspy_config import Language, MultilspyConfig
 from .multilspy_exceptions import MultilspyException
-from .multilspy_utils import PathUtils, FileUtils, TextUtils
-from pathlib import Path, PurePath
-from typing import AsyncIterator, Iterator, List, Dict, Optional, TypedDict, Union, Tuple, cast
+from .multilspy_logger import MultilspyLogger
+from .multilspy_utils import FileUtils, PathUtils, TextUtils
 from .type_helpers import ensure_all_methods_implemented
 
-
 # Serena dependencies
 # We will need to watch out for circular imports, but it's probably better to not
 # move all generic util code from serena into multilspy.
@@ -664,7 +663,7 @@ class LanguageServer:
 
         :param relative_file_path: The relative path of the file that has the symbols
         :param include_body: whether to include the body of the symbols in the result.
-        :return: A list of symbols in the file, and a list of root symbols that represent the tree structure of the symbols. 
+        :return: A list of symbols in the file, and a list of root symbols that represent the tree structure of the symbols.
             Each symbol in hierarchy starting from the roots has a children attribute.
             All symbols will have a location and a children attribute.
         """
@@ -712,6 +711,10 @@ class LanguageServer:
         assert isinstance(response, list)
         root_nodes: List[multilspy_types.UnifiedSymbolInformation] = []
         for item in response:
+            if "range" not in item and "location" not in item:
+                if item["kind"] in [SymbolKind.File, SymbolKind.Module]:
+                    ...
+
             turn_item_into_symbol_with_children(item)
             item = cast(multilspy_types.UnifiedSymbolInformation, item)
             root_nodes.append(item)
@@ -753,7 +756,7 @@ class LanguageServer:
         Will ignore all directories that start with a dot (.) and __pycache__ directories.
         
         Args:
-            start_package_relative_path: if passed, only the symbols within this directory will be considered.
+            start_dir_relative_path: if passed, only the symbols within this directory will be considered.
             include_body: whether to include the body of the symbols in the result.
 
         Returns:
@@ -829,12 +832,17 @@ class LanguageServer:
                     fix_relative_path(root_nodes)
 
                     # Create file symbol
+                    file_rel_path = str(Path(abs_item_path).resolve().relative_to(self.repository_root_path))
+                    with self.open_file(file_rel_path) as file_data:
+                        fileRange = self._get_range_from_file_content(file_data.contents)
                     file_symbol = multilspy_types.UnifiedSymbolInformation( # type: ignore
                         name=os.path.splitext(item)[0],
                         kind=multilspy_types.SymbolKind.File,
+                        range=fileRange,
+                        selectionRange=fileRange,
                         location=multilspy_types.Location(
                             uri=str(pathlib.Path(abs_item_path).as_uri()),
-                            range={"start": {"line": 0, "character": 0}, "end": {"line": 0, "character": 0}},
+                            range=fileRange,
                             absolutePath=str(abs_item_path),
                             relativePath=str(Path(abs_item_path).resolve().relative_to(self.repository_root_path)),
                         ),
@@ -848,7 +856,20 @@ class LanguageServer:
         # Start from the root or the specified directory
         start_path = start_dir_relative_path or "."
         return await process_directory(start_path)
-    
+
+    @staticmethod
+    def _get_range_from_file_content(file_content: str) -> multilspy_types.Range:
+        """
+        Get the range for the given file.
+        """
+        lines = file_content.split("\n")
+        end_line = len(lines)
+        end_column = len(lines[-1])
+        return multilspy_types.Range(
+            start=multilspy_types.Position(line=0, character=0),
+            end=multilspy_types.Position(line=end_line, character=end_column)
+        )
+
     async def request_dir_overview(self, relative_dir_path: str) -> dict[str, list[tuple[str, multilspy_types.SymbolKind, int, int]]]:
         """
         An overview of the given directory. 
@@ -1049,6 +1070,7 @@ class LanguageServer:
         include_imports: bool = True,
         include_self: bool = False,
         include_body: bool = False,
+        include_file_symbols: bool = False,
     ) -> List[multilspy_types.UnifiedSymbolInformation]:
         """
         Finds all symbols that reference the symbol at the given location.
@@ -1064,6 +1086,8 @@ class LanguageServer:
         :param include_self: whether to include the references that is the "input symbol" itself. 
             Only has an effect if the relative_file_path, line and column point to a symbol, for example a definition.
         :param include_body: whether to include the body of the symbols in the result.
+        :param include_file_symbols: whether to include references that are file symbols. This
+            is often a fallback mechanism for when the reference cannot be resolved to a symbol.
         :return: List of symbols that reference the target symbol.
         """
         if not self.server_started:
@@ -1115,9 +1139,41 @@ class LanguageServer:
                                 containing_symbol["location"] = ref
                                 containing_symbol["range"] = ref["range"]
                                 break
-                if containing_symbol is None:
-                    self.logger.log(f"Could not find containing symbol for {ref_path}:{ref_line}:{ref_col}", logging.WARNING)
+
+                # We failed retrieving the symbol, falling back to creating a file symbol
+                if containing_symbol is None and include_file_symbols:
+                    self.logger.log(
+                        f"Could not find containing symbol for {ref_path}:{ref_line}:{ref_col}. Returning file symbol instead",
+                        logging.WARNING
+                    )
+                    fileRange = self._get_range_from_file_content(file_data.contents)
+                    location = multilspy_types.Location(
+                        uri=str(pathlib.Path(os.path.join(self.repository_root_path, ref_path)).as_uri()),
+                        range=fileRange,
+                        absolutePath=str(os.path.join(self.repository_root_path, ref_path)),
+                        relativePath=ref_path,
+                    )
+                    name = os.path.splitext(os.path.basename(ref_path))[0]
+
+                    if include_body:
+                        body = self.retrieve_full_file_content(ref_path)
+                    else:
+                        body = ""
+
+                    containing_symbol = multilspy_types.UnifiedSymbolInformation(
+                        kind=multilspy_types.SymbolKind.File,
+                        range=fileRange,
+                        selectionRange=fileRange,
+                        location=location,
+                        name=name,
+                        children=[],
+                        body=body,
+                    )
+                if containing_symbol is None or not include_file_symbols and containing_symbol["kind"] == multilspy_types.SymbolKind.File:
                     continue
+                
+                assert "location" in containing_symbol
+                assert "selectionRange" in containing_symbol
 
                 # Checking for self-reference
                 if (
@@ -1198,7 +1254,7 @@ class LanguageServer:
                     f"Passing empty lines to request_container_symbol is currently not supported, {relative_file_path=}, {line=}",
                     logging.ERROR,
                 )
-                return
+                return None
 
         symbols, _ = await self.request_document_symbols(relative_file_path)
         
@@ -1220,7 +1276,7 @@ class LanguageServer:
                 assert "range" in location
                 location["absolutePath"] = absolute_file_path
                 location["relativePath"] = relative_file_path
-                location["uri"] = f"file:/{absolute_file_path}"
+                location["uri"] = Path(absolute_file_path).as_uri()
 
         # Allowed container kinds, currently only for Python
         container_symbol_kinds = {
@@ -1610,6 +1666,7 @@ class SyncLanguageServer:
         self, relative_file_path: str, line: int, column: int,
         include_imports: bool = True, include_self: bool = False,
         include_body: bool = False,
+        include_file_symbols: bool = False,
     ) -> List[multilspy_types.UnifiedSymbolInformation]:
         """
         Finds all symbols that reference the symbol at the given location.
@@ -1625,6 +1682,8 @@ class SyncLanguageServer:
         :param include_self: whether to include the references that is the "input symbol" itself. 
             Only has an effect if the relative_file_path, line and column point to a symbol, for example a definition.
         :param include_body: whether to include the body of the symbols in the result.
+        :param include_file_symbols: whether to include references that are file symbols. This
+            is often a fallback mechanism for when the reference cannot be resolved to a symbol.
         :return: List of symbols that reference the target symbol.
         """
         assert self.loop
@@ -1636,6 +1695,7 @@ class SyncLanguageServer:
                 include_imports=include_imports, 
                 include_self=include_self,
                 include_body=include_body,
+                include_file_symbols=include_file_symbols,
             ), 
             self.loop
         ).result()
diff --git a/test/multilspy/test_basic.py b/test/multilspy/test_basic.py
index 78df9341..8b74bcec 100644
--- a/test/multilspy/test_basic.py
+++ b/test/multilspy/test_basic.py
@@ -5,6 +5,7 @@ These tests validate the functionality of the language server APIs
 like request_references using the test repository.
 """
 
+import os
 from pathlib import Path
 
 from multilspy.language_server import SyncLanguageServer
@@ -17,7 +18,7 @@ class TestLanguageServerBasics:
     def test_request_references_user_class(self, language_server: SyncLanguageServer, repo_path: Path):
         """Test request_references on the User class."""
         # Get references to the User class in models.py
-        file_path = str(repo_path / "test_repo" / "models.py")
+        file_path = os.path.join("test_repo", "models.py")
         # Line 31 contains the User class definition
         references = language_server.request_references(file_path, 31, 6)
 
@@ -30,7 +31,7 @@ class TestLanguageServerBasics:
     def test_request_references_item_class(self, language_server: SyncLanguageServer, repo_path: Path):
         """Test request_references on the Item class."""
         # Get references to the Item class in models.py
-        file_path = str(repo_path / "test_repo" / "models.py")
+        file_path = os.path.join("test_repo", "models.py")
         # Line 56 contains the Item class definition
         references = language_server.request_references(file_path, 56, 6)
 
@@ -44,7 +45,7 @@ class TestLanguageServerBasics:
     def test_request_references_function_parameter(self, language_server: SyncLanguageServer, repo_path: Path):
         """Test request_references on a function parameter."""
         # Get references to the id parameter in get_user method
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 24 contains the get_user method with id parameter
         references = language_server.request_references(file_path, 24, 16)
 
@@ -53,7 +54,7 @@ class TestLanguageServerBasics:
 
     def test_request_references_create_user_method(self, language_server: SyncLanguageServer, repo_path: Path):
         # Get references to the create_user method in UserService
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 15 contains the create_user method definition
         references = language_server.request_references(file_path, 15, 9)
 
@@ -62,7 +63,7 @@ class TestLanguageServerBasics:
 
     def test_retrieve_content_around_line(self, language_server: SyncLanguageServer, repo_path: Path):
         """Test retrieve_content_around_line functionality with various scenarios."""
-        file_path = str(repo_path / "test_repo" / "models.py")
+        file_path = os.path.join("test_repo", "models.py")
 
         # Scenario 1: Just a single line (User class definition)
         line_31 = language_server.retrieve_content_around_line(file_path, 31)
diff --git a/test/multilspy/test_symbol_retrieval.py b/test/multilspy/test_symbol_retrieval.py
index afeb7286..dd630b5e 100644
--- a/test/multilspy/test_symbol_retrieval.py
+++ b/test/multilspy/test_symbol_retrieval.py
@@ -7,7 +7,6 @@ These tests focus on the following methods:
 """
 
 import os
-from pathlib import Path
 
 from multilspy.language_server import SyncLanguageServer
 from multilspy.multilspy_types import SymbolKind
@@ -16,10 +15,10 @@ from multilspy.multilspy_types import SymbolKind
 class TestLanguageServerSymbols:
     """Test the language server's symbol-related functionality."""
 
-    def test_request_containing_symbol_function(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_containing_symbol_function(self, language_server: SyncLanguageServer):
         """Test request_containing_symbol for a function."""
         # Test for a position inside the create_user method
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 17 is inside the create_user method body
         containing_symbol = language_server.request_containing_symbol(file_path, 17, 20, include_body=True)
 
@@ -30,9 +29,9 @@ class TestLanguageServerSymbols:
         if "body" in containing_symbol:
             assert containing_symbol["body"].strip().startswith("def create_user(self")
 
-    def test_references_to_variables(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_references_to_variables(self, language_server: SyncLanguageServer):
         """Test request_referencing_symbols for a variable."""
-        file_path = str(repo_path / "test_repo" / "variables.py")
+        file_path = os.path.join("test_repo", "variables.py")
         # Line 75 contains the field status that is later modified
         ref_symbols = language_server.request_referencing_symbols(file_path, 74, 4)
 
@@ -44,10 +43,10 @@ class TestLanguageServerSymbols:
         assert "dataclass_instance" in ref_names
         assert "second_dataclass" in ref_names
 
-    def test_request_containing_symbol_class(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_containing_symbol_class(self, language_server: SyncLanguageServer):
         """Test request_containing_symbol for a class."""
         # Test for a position inside the UserService class but outside any method
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 9 is the class definition line for UserService
         containing_symbol = language_server.request_containing_symbol(file_path, 9, 7)
 
@@ -56,10 +55,10 @@ class TestLanguageServerSymbols:
         assert containing_symbol["name"] == "UserService"
         assert containing_symbol["kind"] == SymbolKind.Class
 
-    def test_request_containing_symbol_nested(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_containing_symbol_nested(self, language_server: SyncLanguageServer):
         """Test request_containing_symbol with nested scopes."""
         # Test for a position inside a method which is inside a class
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 18 is inside the create_user method inside UserService class
         containing_symbol = language_server.request_containing_symbol(file_path, 18, 25)
 
@@ -81,20 +80,20 @@ class TestLanguageServerSymbols:
             assert parent_symbol["name"] == "UserService"
             assert parent_symbol["kind"] == SymbolKind.Class
 
-    def test_request_containing_symbol_none(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_containing_symbol_none(self, language_server: SyncLanguageServer):
         """Test request_containing_symbol for a position with no containing symbol."""
         # Test for a position outside any function/class (e.g., in imports)
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 1 is in imports, not inside any function or class
         containing_symbol = language_server.request_containing_symbol(file_path, 1, 10)
 
         # Should return None or an empty dictionary
         assert containing_symbol is None or containing_symbol == {}
 
-    def test_request_referencing_symbols_function(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_referencing_symbols_function(self, language_server: SyncLanguageServer):
         """Test request_referencing_symbols for a function."""
         # Test referencing symbols for create_user function
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 15 contains the create_user function definition
         ref_symbols = language_server.request_referencing_symbols(file_path, 15, 9)
 
@@ -109,10 +108,10 @@ class TestLanguageServerSymbols:
                 assert "start" in symbol["location"]["range"]
                 assert "end" in symbol["location"]["range"]
 
-    def test_request_referencing_symbols_class(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_referencing_symbols_class(self, language_server: SyncLanguageServer):
         """Test request_referencing_symbols for a class."""
         # Test referencing symbols for User class
-        file_path = str(repo_path / "test_repo" / "models.py")
+        file_path = os.path.join("test_repo", "models.py")
         # Line 31 contains the User class definition
         ref_symbols = language_server.request_referencing_symbols(file_path, 31, 6)
 
@@ -128,10 +127,10 @@ class TestLanguageServerSymbols:
 
         assert len(services_references) > 0
 
-    def test_request_referencing_symbols_parameter(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_referencing_symbols_parameter(self, language_server: SyncLanguageServer):
         """Test request_referencing_symbols for a function parameter."""
         # Test referencing symbols for id parameter in get_user
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 24 contains the get_user method with id parameter
         ref_symbols = language_server.request_referencing_symbols(file_path, 24, 16)
 
@@ -147,12 +146,12 @@ class TestLanguageServerSymbols:
 
         assert len(method_refs) > 0
 
-    def test_request_referencing_symbols_none(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_referencing_symbols_none(self, language_server: SyncLanguageServer):
         """Test request_referencing_symbols for a position with no symbol."""
         # For positions with no symbol, the method might throw an error or return None/empty list
         # We'll modify our test to handle this by using a try-except block
 
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 3 is a blank line or comment
         try:
             ref_symbols = language_server.request_referencing_symbols(file_path, 3, 0)
@@ -164,10 +163,10 @@ class TestLanguageServerSymbols:
             pass
 
     # Tests for request_defining_symbol
-    def test_request_defining_symbol_variable(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_defining_symbol_variable(self, language_server: SyncLanguageServer):
         """Test request_defining_symbol for a variable usage."""
         # Test finding the definition of a symbol in the create_user method
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 21 contains self.users[id] = user
         defining_symbol = language_server.request_defining_symbol(file_path, 21, 10)
 
@@ -182,10 +181,10 @@ class TestLanguageServerSymbols:
         if "location" in defining_symbol and "uri" in defining_symbol["location"]:
             assert "services.py" in defining_symbol["location"]["uri"]
 
-    def test_request_defining_symbol_imported_class(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_defining_symbol_imported_class(self, language_server: SyncLanguageServer):
         """Test request_defining_symbol for an imported class."""
         # Test finding the definition of the 'User' class used in the UserService.create_user method
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 20 references 'User' which was imported from models
         defining_symbol = language_server.request_defining_symbol(file_path, 20, 15)
 
@@ -193,10 +192,10 @@ class TestLanguageServerSymbols:
         assert defining_symbol is not None
         assert defining_symbol.get("name") == "User"
 
-    def test_request_defining_symbol_method_call(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_defining_symbol_method_call(self, language_server: SyncLanguageServer):
         """Test request_defining_symbol for a method call."""
         # Create an example file path for a file that calls UserService.create_user
-        examples_file_path = str(repo_path / "examples" / "user_management.py")
+        examples_file_path = os.path.join("examples", "user_management.py")
 
         # Find the line number where create_user is called
         # This could vary, so we'll use a relative position that makes sense
@@ -217,20 +216,20 @@ class TestLanguageServerSymbols:
 
             warnings.warn("Could not verify method call definition - file structure may differ from expected")
 
-    def test_request_defining_symbol_none(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_defining_symbol_none(self, language_server: SyncLanguageServer):
         """Test request_defining_symbol for a position with no symbol."""
         # Test for a position with no symbol (e.g., whitespace or comment)
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 3 is a blank line
         defining_symbol = language_server.request_defining_symbol(file_path, 3, 0)
 
         # Should return None for positions with no symbol
         assert defining_symbol is None
 
-    def test_request_containing_symbol_variable(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_containing_symbol_variable(self, language_server: SyncLanguageServer):
         """Test request_containing_symbol where the symbol is a variable."""
         # Test for a position inside a variable definition
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
         # Line 74 defines the 'user' variable
         containing_symbol = language_server.request_containing_symbol(file_path, 73, 1)
 
@@ -239,10 +238,10 @@ class TestLanguageServerSymbols:
         assert containing_symbol["name"] == "user_var_str"
         assert containing_symbol["kind"] == SymbolKind.Variable
 
-    def test_request_defining_symbol_nested_function(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_defining_symbol_nested_function(self, language_server: SyncLanguageServer):
         """Test request_defining_symbol for a nested function or closure."""
         # Use the existing nested.py file which contains nested classes and methods
-        file_path = str(repo_path / "test_repo" / "nested.py")
+        file_path = os.path.join("test_repo", "nested.py")
 
         # Test 1: Find definition of nested method - line with 'b = OuterClass().NestedClass().find_me()'
         defining_symbol = language_server.request_defining_symbol(file_path, 15, 35)  # Position of find_me() call
@@ -289,12 +288,12 @@ class TestLanguageServerSymbols:
         assert defining_symbol.get("name") == "func_within_func"
         assert defining_symbol.get("kind") == SymbolKind.Function.value
 
-    def test_symbol_methods_integration(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_symbol_methods_integration(self, language_server: SyncLanguageServer):
         """Test the integration between different symbol-related methods."""
         # This test demonstrates using the various symbol methods together
         # by finding a symbol and then checking its definition
 
-        file_path = str(repo_path / "test_repo" / "services.py")
+        file_path = os.path.join("test_repo", "services.py")
 
         # First approach: Use a method from the UserService class
         # Step 1: Find a method we know exists
@@ -337,7 +336,7 @@ class TestLanguageServerSymbols:
 
                 warnings.warn("Could not verify container hierarchy - implementation detail")
 
-    def test_symbol_tree_structure(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_symbol_tree_structure(self, language_server: SyncLanguageServer):
         """Test that the symbol tree structure is correctly built."""
         # Get all symbols in the test file
         repo_structure = language_server.request_full_symbol_tree()
@@ -361,13 +360,13 @@ class TestLanguageServerSymbols:
         if "location" in user_management_node and "relativePath" in user_management_node["location"]:
             user_management_rel_path = user_management_node["location"]["relativePath"]
             assert user_management_rel_path == os.path.join("examples", "user_management.py")
-            _, user_management_roots = language_server.request_document_symbols(str(repo_path / "examples" / "user_management.py"))
+            _, user_management_roots = language_server.request_document_symbols(os.path.join("examples", "user_management.py"))
             assert user_management_roots == user_management_node["children"]
 
-    def test_symbol_tree_structure_subdir(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_symbol_tree_structure_subdir(self, language_server: SyncLanguageServer):
         """Test that the symbol tree structure is correctly built."""
         # Get all symbols in the test file
-        examples_package_roots = language_server.request_full_symbol_tree(start_package_relative_path=str(repo_path / "examples"))
+        examples_package_roots = language_server.request_full_symbol_tree(start_package_relative_path="examples")
         assert len(examples_package_roots) == 1
         examples_package = examples_package_roots[0]
         assert examples_package["name"] == "examples"
@@ -381,10 +380,10 @@ class TestLanguageServerSymbols:
         if "location" in user_management_node and "relativePath" in user_management_node["location"]:
             user_management_rel_path = user_management_node["location"]["relativePath"]
             assert user_management_rel_path == os.path.join("examples", "user_management.py")
-            _, user_management_roots = language_server.request_document_symbols(str(repo_path / "examples" / "user_management.py"))
+            _, user_management_roots = language_server.request_document_symbols(os.path.join("examples", "user_management.py"))
             assert user_management_roots == user_management_node["children"]
 
-    def test_request_dir_overview(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_dir_overview(self, language_server: SyncLanguageServer):
         """Test that request_dir_overview returns correct symbol information for files in a directory."""
         # Get overview of the examples directory
         overview = language_server.request_dir_overview("test_repo")
@@ -408,7 +407,7 @@ class TestLanguageServerSymbols:
         for symbol in expected_symbols:
             assert symbol in services_symbols
 
-    def test_request_document_overview(self, language_server: SyncLanguageServer, repo_path: Path):
+    def test_request_document_overview(self, language_server: SyncLanguageServer):
         """Test that request_document_overview returns correct symbol information for a file."""
         # Get overview of the user_management.py file
         overview = language_server.request_document_overview(os.path.join("examples", "user_management.py"))
@@ -416,3 +415,21 @@ class TestLanguageServerSymbols:
         # Verify that we have entries for both files
         symbol_names = {s_info[0] for s_info in overview}
         assert {"UserStats", "UserManager", "process_user_data", "main"}.issubset(symbol_names)
+
+    def test_containing_symbol_of_var_is_file(self, language_server: SyncLanguageServer):
+        """Test that the containing symbol of a variable is the file itself."""
+        # Get the containing symbol of a variable in a file
+        file_path = os.path.join("test_repo", "services.py")
+        # import of typing
+        references_to_typing = language_server.request_referencing_symbols(
+            file_path, 4, 6, include_imports=False, include_file_symbols=True
+        )
+        assert {ref["kind"] for ref in references_to_typing} == {SymbolKind.File}
+        assert {ref["body"] for ref in references_to_typing} == {""}
+
+        # now include bodies
+        references_to_typing = language_server.request_referencing_symbols(
+            file_path, 4, 6, include_imports=False, include_file_symbols=True, include_body=True
+        )
+        assert {ref["kind"] for ref in references_to_typing} == {SymbolKind.File}
+        assert references_to_typing[0]["body"]

From 913a90b3760919b520be067a770c8fda39864116 Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 17:10:55 +0200
Subject: [PATCH 2/9] Minor

---
 .vscode/settings.json |  5 ++++-
 scripts/agno_agent.py | 11 ++++++-----
 src/serena/agno.py    |  3 ++-
 3 files changed, 12 insertions(+), 7 deletions(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 5d3ef653..b086ceaf 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,7 +1,10 @@
 {
     "cSpell.words": [
+        "agno",
+        "genai",
         "langsrv",
         "multilspy",
-        "pixi"
+        "pixi",
+        "sensai"
     ]
 }
\ No newline at end of file
diff --git a/scripts/agno_agent.py b/scripts/agno_agent.py
index 98271347..25b61ce1 100644
--- a/scripts/agno_agent.py
+++ b/scripts/agno_agent.py
@@ -1,11 +1,12 @@
 import os
 from logging import Logger
 
-from agno.agent import Agent
-from agno.memory import AgentMemory
-from agno.models.anthropic import Claude
-from agno.models.google import Gemini
-from agno.playground import Playground, serve_playground_app
+from agno.agent.agent import Agent
+from agno.memory.agent import AgentMemory
+from agno.models.anthropic.claude import Claude
+from agno.models.google.gemini import Gemini
+from agno.playground.playground import Playground
+from agno.playground.serve import serve_playground_app
 from dotenv import load_dotenv
 from sensai.util import logging
 from sensai.util.helper import mark_used
diff --git a/src/serena/agno.py b/src/serena/agno.py
index 982cc29d..54ccd166 100644
--- a/src/serena/agno.py
+++ b/src/serena/agno.py
@@ -1,7 +1,8 @@
 import logging
 from typing import Any
 
-from agno.tools import Function, Toolkit
+from agno.tools.function import Function
+from agno.tools.toolkit import Toolkit
 
 from serena.agent import SerenaAgent, Tool
 

From 3defcad8195ef76cde5d462e270564d405aa900a Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 17:36:32 +0200
Subject: [PATCH 3/9] uv lock

---
 uv.lock | 1831 -------------------------------------------------------
 1 file changed, 1831 deletions(-)

diff --git a/uv.lock b/uv.lock
index ac842b47..2e938f2a 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2,18 +2,6 @@ version = 1
 revision = 1
 requires-python = "==3.11.*"
 
-[[package]]
-name = "accessible-pygments"
-version = "0.0.5"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "pygments" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/bc/c1/bbac6a50d02774f91572938964c582fff4270eee73ab822a4aeea4d8b11b/accessible_pygments-0.0.5.tar.gz", hash = "sha256:40918d3e6a2b619ad424cb91e556bd3bd8865443d9f22f1dcdf79e33c8046872", size = 1377899 }
-wheels = [
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-]
-
 [[package]]
 name = "agno"
 version = "1.2.6"
@@ -37,15 +25,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/4d/ca/c0bf8045f6ca7cf8e99fe2f60c1162eca7f056c6b447fad27e0fd81e88ec/agno-1.2.6-py3-none-any.whl", hash = "sha256:b008416f01f4a6b2ff106777586ccc0d93d50f114944140dd95e2ff8adf7802a", size = 586946 },
 ]
 
-[[package]]
-name = "alabaster"
-version = "0.7.16"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/c9/3e/13dd8e5ed9094e734ac430b5d0eb4f2bb001708a8b7856cbf8e084e001ba/alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65", size = 23776 }
-wheels = [
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-
 [[package]]
 name = "annotated-types"
 version = "0.7.0"
@@ -87,89 +66,6 @@ wheels = [
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 ]
 
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-dependencies = [
-    { name = "apeye-core" },
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-version = "1.0.3"
-source = { registry = "https://pypi.org/simple" }
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-]
-
-[[package]]
-name = "uri-template"
-version = "1.3.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/31/c7/0336f2bd0bcbada6ccef7aaa25e443c118a704f828a0620c6fa0207c1b64/uri-template-1.3.0.tar.gz", hash = "sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7", size = 21678 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/e7/00/3fca040d7cf8a32776d3d81a00c8ee7457e00f80c649f1e4a863c8321ae9/uri_template-1.3.0-py3-none-any.whl", hash = "sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363", size = 11140 },
-]
-
 [[package]]
 name = "urllib3"
 version = "2.3.0"
@@ -2937,20 +1174,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/61/14/33a3a1352cfa71812a3a21e8c9bfb83f60b0011f5e36f2b1399d51928209/uvicorn-0.34.0-py3-none-any.whl", hash = "sha256:023dc038422502fa28a09c7a30bf2b6991512da7dcdb8fd35fe57cfc154126f4", size = 62315 },
 ]
 
-[[package]]
-name = "virtualenv"
-version = "20.29.3"
-source = { registry = "https://pypi.org/simple" }
-dependencies = [
-    { name = "distlib" },
-    { name = "filelock" },
-    { name = "platformdirs" },
-]
-sdist = { url = "https://files.pythonhosted.org/packages/c7/9c/57d19fa093bcf5ac61a48087dd44d00655f85421d1aa9722f8befbf3f40a/virtualenv-20.29.3.tar.gz", hash = "sha256:95e39403fcf3940ac45bc717597dba16110b74506131845d9b687d5e73d947ac", size = 4320280 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/c2/eb/c6db6e3001d58c6a9e67c74bb7b4206767caa3ccc28c6b9eaf4c23fb4e34/virtualenv-20.29.3-py3-none-any.whl", hash = "sha256:3e3d00f5807e83b234dfb6122bf37cfadf4be216c53a49ac059d02414f819170", size = 4301458 },
-]
-
 [[package]]
 name = "wcwidth"
 version = "0.2.13"
@@ -2960,33 +1183,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859", size = 34166 },
 ]
 
-[[package]]
-name = "webcolors"
-version = "24.11.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/7b/29/061ec845fb58521848f3739e466efd8250b4b7b98c1b6c5bf4d40b419b7e/webcolors-24.11.1.tar.gz", hash = "sha256:ecb3d768f32202af770477b8b65f318fa4f566c22948673a977b00d589dd80f6", size = 45064 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/60/e8/c0e05e4684d13459f93d312077a9a2efbe04d59c393bc2b8802248c908d4/webcolors-24.11.1-py3-none-any.whl", hash = "sha256:515291393b4cdf0eb19c155749a096f779f7d909f7cceea072791cb9095b92e9", size = 14934 },
-]
-
-[[package]]
-name = "webencodings"
-version = "0.5.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/0b/02/ae6ceac1baeda530866a85075641cec12989bd8d31af6d5ab4a3e8c92f47/webencodings-0.5.1.tar.gz", hash = "sha256:b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923", size = 9721 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl", hash = "sha256:a0af1213f3c2226497a97e2b3aa01a7e4bee4f403f95be16fc9acd2947514a78", size = 11774 },
-]
-
-[[package]]
-name = "websocket-client"
-version = "1.8.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/e6/30/fba0d96b4b5fbf5948ed3f4681f7da2f9f64512e1d303f94b4cc174c24a5/websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da", size = 54648 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/5a/84/44687a29792a70e111c5c477230a72c4b957d88d16141199bf9acb7537a3/websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526", size = 58826 },
-]
-
 [[package]]
 name = "websockets"
 version = "15.0.1"
@@ -3006,30 +1202,3 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/98/93/e36c73f78400a65f5e236cd376713c34182e6663f6889cd45a4a04d8f203/websockets-15.0.1-cp311-cp311-win_amd64.whl", hash = "sha256:27ccee0071a0e75d22cb35849b1db43f2ecd3e161041ac1ee9d2352ddf72f065", size = 176828 },
     { url = "https://files.pythonhosted.org/packages/fa/a8/5b41e0da817d64113292ab1f8247140aac61cbf6cfd085d6a0fa77f4984f/websockets-15.0.1-py3-none-any.whl", hash = "sha256:f7a866fbc1e97b5c617ee4116daaa09b722101d4a3c170c787450ba409f9736f", size = 169743 },
 ]
-
-[[package]]
-name = "wheel"
-version = "0.45.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/8a/98/2d9906746cdc6a6ef809ae6338005b3f21bb568bea3165cfc6a243fdc25c/wheel-0.45.1.tar.gz", hash = "sha256:661e1abd9198507b1409a20c02106d9670b2576e916d58f520316666abca6729", size = 107545 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/0b/2c/87f3254fd8ffd29e4c02732eee68a83a1d3c346ae39bc6822dcbcb697f2b/wheel-0.45.1-py3-none-any.whl", hash = "sha256:708e7481cc80179af0e556bbf0cc00b8444c7321e2700b8d8580231d13017248", size = 72494 },
-]
-
-[[package]]
-name = "widgetsnbextension"
-version = "4.0.13"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/56/fc/238c424fd7f4ebb25f8b1da9a934a3ad7c848286732ae04263661eb0fc03/widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6", size = 1164730 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/21/02/88b65cc394961a60c43c70517066b6b679738caf78506a5da7b88ffcb643/widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71", size = 2335872 },
-]
-
-[[package]]
-name = "zipp"
-version = "3.21.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/3f/50/bad581df71744867e9468ebd0bcd6505de3b275e06f202c2cb016e3ff56f/zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4", size = 24545 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/b7/1a/7e4798e9339adc931158c9d69ecc34f5e6791489d469f5e50ec15e35f458/zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931", size = 9630 },
-]

From 1b2bfc0e3a581c4b6aecd610c53ff63afad5b92a Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 17:37:16 +0200
Subject: [PATCH 4/9] Made agno work with memory

---
 .gitignore            |  4 +++-
 scripts/agno_agent.py | 13 +++++++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 754b0195..886b8d49 100644
--- a/.gitignore
+++ b/.gitignore
@@ -144,4 +144,6 @@ pylint.html
 /src/multilspy/language_servers/*/static
 
 # Cache is in .multilspy 
-**/.multilspy/**
\ No newline at end of file
+**/.multilspy/**
+
+tmp/
diff --git a/scripts/agno_agent.py b/scripts/agno_agent.py
index 25b61ce1..a105a3fa 100644
--- a/scripts/agno_agent.py
+++ b/scripts/agno_agent.py
@@ -7,6 +7,7 @@ from agno.models.anthropic.claude import Claude
 from agno.models.google.gemini import Gemini
 from agno.playground.playground import Playground
 from agno.playground.serve import serve_playground_app
+from agno.storage.agent.sqlite import SqliteAgentStorage
 from dotenv import load_dotenv
 from sensai.util import logging
 from sensai.util.helper import mark_used
@@ -24,12 +25,24 @@ load_dotenv()
 project_file_path = "../myproject.yml"
 serena_agent = SerenaAgent(project_file_path, start_language_server=True)
 
+# Even though we don't want to keep history between sessions,
+# for the agno ui to work as a conversation, we a persistent storage on disk
+# This storage should be deleted between sessions.
+# Note that this might collide with custom options for the agent, like adding vector-search based tools.
+# See here for an explanation: https://www.reddit.com/r/agno/comments/1jk6qea/regarding_the_built_in_memory/
+sql_db_path = os.path.join("tmp", "agent_storage.db")
+os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
+# delete the db file if it exists
+if os.path.exists(sql_db_path):
+    os.remove(sql_db_path)
+
 model = Claude(id="claude-3-7-sonnet-20250219")
 # model = Gemini(id="gemini-2.5-pro-exp-03-25")
 
 agno_agent = Agent(
     name="Serena",
     model=model,
+    storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
     description="A fully-featured coding assistant",
     tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
     show_tool_calls=False,

From 4eb4a26374028647868e24dab90b7f822105ed80 Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 17:37:45 +0200
Subject: [PATCH 5/9] Gitignore

---
 .gitignore | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.gitignore b/.gitignore
index 886b8d49..b04a9643 100644
--- a/.gitignore
+++ b/.gitignore
@@ -147,3 +147,5 @@ pylint.html
 **/.multilspy/**
 
 tmp/
+
+.serena/

From efbea42e3903bb8074d92081beb660706fb36041 Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 18:34:15 +0200
Subject: [PATCH 6/9] Made tool selection configurable

More things:
- list tools using .subclasses instead of inspect
- entrypoint for listing tools
- util for listing selected tools
- documentation
---
 README.md                     |  2 +-
 myproject.demo.yml            | 45 ++++++++++++++++++++++++++++++-
 pyproject.toml                |  3 ++-
 scripts/agno_agent.py         | 51 +++++++++++++++++------------------
 scripts/list_tools.py         | 10 -------
 src/serena/agent.py           | 39 ++++++++++++++++++++-------
 src/serena/util/inspection.py | 12 +++++++++
 7 files changed, 113 insertions(+), 49 deletions(-)
 delete mode 100644 scripts/list_tools.py
 create mode 100644 src/serena/util/inspection.py

diff --git a/README.md b/README.md
index b1714f6c..9225a0b9 100644
--- a/README.md
+++ b/README.md
@@ -74,7 +74,7 @@ We thus built Serena with the prospect of being able to cancel most other subscr
     "mcpServers": {
         "serena": {
             "command": "/abs/path/to/uv",
-            "args": ["run", "--directory", "/abs/path/to/serena", "serena", "/abs/path/to/myproject.yml"]
+            "args": ["run", "--directory", "/abs/path/to/serena", "serena-mcp-server", "/abs/path/to/myproject.yml"]
         }
     }
 }
diff --git a/myproject.demo.yml b/myproject.demo.yml
index 4ddcd76f..b5272299 100644
--- a/myproject.demo.yml
+++ b/myproject.demo.yml
@@ -4,7 +4,50 @@ project_root: /path/to/project
 language: python
 # list of directories to ignore: either names (e.g. "temp") or relative paths (e.g. "build/foo")
 ignored_dirs: [".git", "temp"]
-# whether to open a graphical window with Serena's logs (not supported on MacOS)
+
+# list of tool names to exclude. We recommend not excluding any tools, see the readme for more details.
+# 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 serena-list-tools`.
+#
+# check_onboarding_performed
+# create_text_file
+# delete_lines
+# delete_memory
+# execute_shell_command
+# find_referencing_symbols
+# find_symbol
+# get_dir_overview
+# get_document_overview
+# insert_after_symbol
+# insert_at_line
+# insert_before_symbol
+# list_dir
+# list_memories
+# onboarding
+# prepare_for_new_conversation
+# read_file
+# read_memory
+# replace_symbol_body
+# search_in_all_code
+# summarize_changes
+# think_about_collected_information
+# think_about_task_adherence
+# think_about_whether_you_are_done
+# write_memory
+excluded_tools: []
+
+
+
+# Whether to open a graphical window with Serena's logs (not supported on MacOS).
+# This is useful both for troubleshooting and for monitoring the tool calls,
+# especially when using the agno playground, since the tool calls are not always shown,
+# and the input params are never shown in the agno UI.
+# When used as MCP server for Claude Desktop, the logs are primarily for troubleshooting.
+# Note: unfortunately, the various entities starting the Serena server or agent do so in
+# mysterious ways, often starting multiple instances of the process without shutting down
+# previous instances. This leads to multiple log windows being opened, and only the last
+# window being updated. Since we can't control how agno or Claude Desktop starts Serena, we have to live with this limitation for now.
 gui_log_window: True
 # minimum log level for the GUI log window (10 = debug, 20 = info, 30 = warning, 40 = error)
 gui_log_level: 20
diff --git a/pyproject.toml b/pyproject.toml
index 55e13a54..e03e4569 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,7 +33,8 @@ dependencies = [
 ]
 
 [project.scripts]
-serena = "serena.mcp:start_mcp_server"
+serena-mcp-server = "serena.mcp:start_mcp_server"
+serena-list-tools = "serena.agent:print_tool_overview"
 
 [project.license]
 text = "MIT"
diff --git a/scripts/agno_agent.py b/scripts/agno_agent.py
index a105a3fa..eb318c2f 100644
--- a/scripts/agno_agent.py
+++ b/scripts/agno_agent.py
@@ -1,19 +1,13 @@
 import os
 from logging import Logger
 
-from agno.agent.agent import Agent
-from agno.memory.agent import AgentMemory
 from agno.models.anthropic.claude import Claude
 from agno.models.google.gemini import Gemini
-from agno.playground.playground import Playground
-from agno.playground.serve import serve_playground_app
-from agno.storage.agent.sqlite import SqliteAgentStorage
 from dotenv import load_dotenv
 from sensai.util import logging
 from sensai.util.helper import mark_used
 
 from serena.agent import SerenaAgent
-from serena.agno import SerenaAgnoToolkit
 
 mark_used(Gemini, Claude)
 
@@ -36,27 +30,30 @@ os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
 if os.path.exists(sql_db_path):
     os.remove(sql_db_path)
 
-model = Claude(id="claude-3-7-sonnet-20250219")
-# model = Gemini(id="gemini-2.5-pro-exp-03-25")
+for tool_name in serena_agent.list_tool_names():
+    print(tool_name)
 
-agno_agent = Agent(
-    name="Serena",
-    model=model,
-    storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
-    description="A fully-featured coding assistant",
-    tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
-    show_tool_calls=False,
-    markdown=True,
-    system_message=serena_agent.prompt_factory.create_system_prompt(),
-    read_tool_call_history=False,
-    telemetry=False,
-    memory=AgentMemory(),
-    add_history_to_messages=True,
-    num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
-)
+# model = Claude(id="claude-3-7-sonnet-20250219")
+# # model = Gemini(id="gemini-2.5-pro-exp-03-25")
 
-# The app object must be in the module scope so that the server can access it for hot reloading
-app = Playground(agents=[agno_agent]).get_app()
+# agno_agent = Agent(
+#     name="Serena",
+#     model=model,
+#     storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
+#     description="A fully-featured coding assistant",
+#     tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
+#     show_tool_calls=False,
+#     markdown=True,
+#     system_message=serena_agent.prompt_factory.create_system_prompt(),
+#     read_tool_call_history=False,
+#     telemetry=False,
+#     memory=AgentMemory(),
+#     add_history_to_messages=True,
+#     num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
+# )
 
-if __name__ == "__main__":
-    serve_playground_app("agno_agent:app", reload=False)
+# # The app object must be in the module scope so that the server can access it for hot reloading
+# app = Playground(agents=[agno_agent]).get_app()
+
+# if __name__ == "__main__":
+#     serve_playground_app("agno_agent:app", reload=False)
diff --git a/scripts/list_tools.py b/scripts/list_tools.py
deleted file mode 100644
index 1dfafbd5..00000000
--- a/scripts/list_tools.py
+++ /dev/null
@@ -1,10 +0,0 @@
-from serena.agent import SerenaAgent
-
-if __name__ == "__main__":
-    agent = SerenaAgent("myproject.yml")
-    tools = {}
-    for tool in agent.tools.values():
-        tools[tool.get_name()] = tool
-    for tool_name in sorted(tools.keys()):
-        tool = tools[tool_name]
-        print(f" * `{tool_name}`: {tool.get_tool_description().strip()}")
diff --git a/src/serena/agent.py b/src/serena/agent.py
index 725b6658..e4c8557f 100644
--- a/src/serena/agent.py
+++ b/src/serena/agent.py
@@ -11,7 +11,7 @@ import traceback
 import warnings
 from abc import ABC
 from collections import defaultdict
-from collections.abc import Callable, Iterator
+from collections.abc import Callable, Generator, Iterable, Iterator
 from contextlib import contextmanager
 from logging import Logger
 from pathlib import Path
@@ -29,6 +29,7 @@ from serena.gui_log_viewer import GuiLogViewer, GuiLogViewerHandler
 from serena.llm.prompt_factory import PromptFactory
 from serena.symbol import SymbolLocation, SymbolManager
 from serena.util.file_system import scan_directory
+from serena.util.inspection import iter_subclasses
 from serena.util.shell import execute_shell_command
 
 log = logging.getLogger(__name__)
@@ -87,11 +88,12 @@ class SerenaAgent:
         self.memories_manager = MemoriesManager(memories_dir)
 
         # find all tool classes and instantiate them
+        excluded_tools = project_config.get("excluded_tools", [])
         self.tools: dict[type[Tool], Tool] = {}
-        tool_classes = [
-            cls for name, cls in inspect.getmembers(sys.modules[__name__], inspect.isclass) if issubclass(cls, Tool) and cls is not Tool
-        ]
-        for tool_class in tool_classes:
+        for tool_class in iter_tool_classes():
+            if (tool_name := tool_class.get_name()) in excluded_tools:
+                log.info(f"Skipping tool {tool_name} because it is in the exclude list")
+                continue
             tool_instance = tool_class(self)
             self.tools[tool_class] = tool_instance
         log.info(f"Loaded tools: {', '.join([tool.get_name() for tool in self.tools.values()])}")
@@ -101,11 +103,12 @@ class SerenaAgent:
             log.info("Starting the language server ...")
             self.language_server.start()
 
-        self._is_initialized = True
-
     def get_tool(self, tool_class: type[TTool]) -> TTool:
         return self.tools[tool_class]  # type: ignore
 
+    def print_tool_overview(self) -> None:
+        _print_tool_overview(self.tools.values())
+
     def get_serena_managed_dir(self) -> str:
         return os.path.join(self.project_root, ".serena")
 
@@ -195,8 +198,9 @@ class Tool(Component):
             raise Exception(f"{self} does not define method apply")
         return apply_fn
 
-    def get_tool_description(self) -> str:
-        docstring = self.__class__.__doc__
+    @classmethod
+    def get_tool_description(cls) -> str:
+        docstring = cls.__doc__
         if docstring is None:
             return ""
         return docstring.strip()
@@ -878,3 +882,20 @@ class ExecuteShellCommandTool(Tool):
         result = execute_shell_command(command, cwd=_cwd, capture_stderr=capture_stderr)
         result = result.json()
         return self._limit_length(result, max_answer_chars)
+
+
+def iter_tool_classes() -> Generator[type[Tool], None, None]:
+    return iter_subclasses(Tool)
+
+
+def print_tool_overview() -> None:
+    _print_tool_overview(iter_tool_classes())
+
+
+def _print_tool_overview(tools: Iterable[type[Tool] | Tool]) -> None:
+    tool_dict: dict[str, type[Tool] | Tool] = {}
+    for tool in tools:
+        tool_dict[tool.get_name()] = tool
+    for tool_name in sorted(tool_dict.keys()):
+        tool = tool_dict[tool_name]
+        print(f" * `{tool_name}`: {tool.get_tool_description().strip()}")
diff --git a/src/serena/util/inspection.py b/src/serena/util/inspection.py
new file mode 100644
index 00000000..36cffbe7
--- /dev/null
+++ b/src/serena/util/inspection.py
@@ -0,0 +1,12 @@
+from collections.abc import Generator
+from typing import TypeVar
+
+T = TypeVar("T")
+
+
+def iter_subclasses(cls: type[T], recursive: bool = True) -> Generator[type[T], None, None]:
+    """Iterate over all subclasses of a class. If recursive is True, also iterate over all subclasses of all subclasses."""
+    for subclass in cls.__subclasses__():
+        yield subclass
+        if recursive:
+            yield from iter_subclasses(subclass, recursive)

From 83f39564cc0b05b5ff2ec34cc364345487cf98b5 Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 18:38:25 +0200
Subject: [PATCH 7/9] Readme, minor

---
 README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9225a0b9..3caa92d6 100644
--- a/README.md
+++ b/README.md
@@ -169,7 +169,8 @@ without modifying the codebase, you can consider disabling the editing tools in
 In general, be sure to back up your work and use a version control system in order to avoid
 losing any work.
 
-Here a complete list of Serena's tools:
+Here a complete list of Serena's tools
+(you can get an up-to-date list by running `uv run serena-list-tools`)
 
 * `check_onboarding_performed`: Checks whether the onboarding was already performed.
 * `create_text_file`: Creates/overwrites a file in the project directory.

From e6bf952cf6a191a2bad64d6a4eeaace9199dd95b Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 18:49:36 +0200
Subject: [PATCH 8/9] Restored accidentally deleted agno script

---
 scripts/agno_agent.py | 51 +++++++++++++++++++++++--------------------
 1 file changed, 27 insertions(+), 24 deletions(-)

diff --git a/scripts/agno_agent.py b/scripts/agno_agent.py
index eb318c2f..3b7e48c1 100644
--- a/scripts/agno_agent.py
+++ b/scripts/agno_agent.py
@@ -1,13 +1,19 @@
 import os
 from logging import Logger
 
+from agno.agent.agent import Agent
+from agno.memory.agent import AgentMemory
 from agno.models.anthropic.claude import Claude
 from agno.models.google.gemini import Gemini
+from agno.playground.playground import Playground
+from agno.playground.serve import serve_playground_app
+from agno.storage.sqlite import SqliteStorage
 from dotenv import load_dotenv
 from sensai.util import logging
 from sensai.util.helper import mark_used
 
 from serena.agent import SerenaAgent
+from serena.agno import SerenaAgnoToolkit
 
 mark_used(Gemini, Claude)
 
@@ -30,30 +36,27 @@ os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
 if os.path.exists(sql_db_path):
     os.remove(sql_db_path)
 
-for tool_name in serena_agent.list_tool_names():
-    print(tool_name)
+model = Claude(id="claude-3-7-sonnet-20250219")
+# model = Gemini(id="gemini-2.5-pro-exp-03-25")
 
-# model = Claude(id="claude-3-7-sonnet-20250219")
-# # model = Gemini(id="gemini-2.5-pro-exp-03-25")
+agno_agent = Agent(
+    name="Serena",
+    model=model,
+    storage=SqliteStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
+    description="A fully-featured coding assistant",
+    tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
+    show_tool_calls=False,
+    markdown=True,
+    system_message=serena_agent.prompt_factory.create_system_prompt(),
+    read_tool_call_history=False,
+    telemetry=False,
+    memory=AgentMemory(),
+    add_history_to_messages=True,
+    num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
+)
 
-# agno_agent = Agent(
-#     name="Serena",
-#     model=model,
-#     storage=SqliteAgentStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
-#     description="A fully-featured coding assistant",
-#     tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
-#     show_tool_calls=False,
-#     markdown=True,
-#     system_message=serena_agent.prompt_factory.create_system_prompt(),
-#     read_tool_call_history=False,
-#     telemetry=False,
-#     memory=AgentMemory(),
-#     add_history_to_messages=True,
-#     num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
-# )
+# The app object must be in the module scope so that the server can access it for hot reloading
+app = Playground(agents=[agno_agent]).get_app()
 
-# # The app object must be in the module scope so that the server can access it for hot reloading
-# app = Playground(agents=[agno_agent]).get_app()
-
-# if __name__ == "__main__":
-#     serve_playground_app("agno_agent:app", reload=False)
+if __name__ == "__main__":
+    serve_playground_app("agno_agent:app", reload=False)

From 1c4aa6ca1033dff06a405293051933c21000f6e0 Mon Sep 17 00:00:00 2001
From: Michael Panchenko <michael.panchenko@oraios-ai.de>
Date: Tue, 1 Apr 2025 19:17:21 +0200
Subject: [PATCH 9/9] Pass project-file to agno_agent via cli

---
 scripts/agno_agent.py | 83 +++++++++++++++++++++++++------------------
 1 file changed, 48 insertions(+), 35 deletions(-)

diff --git a/scripts/agno_agent.py b/scripts/agno_agent.py
index 3b7e48c1..612ad1ea 100644
--- a/scripts/agno_agent.py
+++ b/scripts/agno_agent.py
@@ -1,6 +1,7 @@
 import os
 from logging import Logger
 
+import click
 from agno.agent.agent import Agent
 from agno.memory.agent import AgentMemory
 from agno.models.anthropic.claude import Claude
@@ -9,6 +10,7 @@ from agno.playground.playground import Playground
 from agno.playground.serve import serve_playground_app
 from agno.storage.sqlite import SqliteStorage
 from dotenv import load_dotenv
+from fastapi import FastAPI
 from sensai.util import logging
 from sensai.util.helper import mark_used
 
@@ -22,41 +24,52 @@ Logger.root.setLevel(logging.INFO)
 
 load_dotenv()
 
-project_file_path = "../myproject.yml"
-serena_agent = SerenaAgent(project_file_path, start_language_server=True)
-
-# Even though we don't want to keep history between sessions,
-# for the agno ui to work as a conversation, we a persistent storage on disk
-# This storage should be deleted between sessions.
-# Note that this might collide with custom options for the agent, like adding vector-search based tools.
-# See here for an explanation: https://www.reddit.com/r/agno/comments/1jk6qea/regarding_the_built_in_memory/
-sql_db_path = os.path.join("tmp", "agent_storage.db")
-os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
-# delete the db file if it exists
-if os.path.exists(sql_db_path):
-    os.remove(sql_db_path)
-
-model = Claude(id="claude-3-7-sonnet-20250219")
-# model = Gemini(id="gemini-2.5-pro-exp-03-25")
-
-agno_agent = Agent(
-    name="Serena",
-    model=model,
-    storage=SqliteStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
-    description="A fully-featured coding assistant",
-    tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
-    show_tool_calls=False,
-    markdown=True,
-    system_message=serena_agent.prompt_factory.create_system_prompt(),
-    read_tool_call_history=False,
-    telemetry=False,
-    memory=AgentMemory(),
-    add_history_to_messages=True,
-    num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
-)
-
 # The app object must be in the module scope so that the server can access it for hot reloading
-app = Playground(agents=[agno_agent]).get_app()
+app: FastAPI | None = None
+
+
+@click.command()
+@click.option("--project-file", default="../myproject.yml", help="Path to the project configuration YAML file")
+def main(project_file):
+    global app  # noqa: PLW0603
+    serena_agent = SerenaAgent(project_file, start_language_server=True)
+
+    # Even though we don't want to keep history between sessions,
+    # for the agno ui to work as a conversation, we a persistent storage on disk
+    # This storage should be deleted between sessions.
+    # Note that this might collide with custom options for the agent, like adding vector-search based tools.
+    # See here for an explanation: https://www.reddit.com/r/agno/comments/1jk6qea/regarding_the_built_in_memory/
+    sql_db_path = os.path.join("tmp", "agent_storage.db")
+    os.makedirs(os.path.dirname(sql_db_path), exist_ok=True)
+    # delete the db file if it exists
+    if os.path.exists(sql_db_path):
+        os.remove(sql_db_path)
+
+    model = Claude(id="claude-3-7-sonnet-20250219")
+    # Or use any other model supported by agno, e.g. the newest Gemini:
+    # model = Gemini(id="gemini-2.5-pro-exp-03-25")
+
+    agno_agent = Agent(
+        name="Serena",
+        model=model,
+        # See explanation above on why storage is needed
+        storage=SqliteStorage(table_name="serena_agent_sessions", db_file=sql_db_path),
+        description="A fully-featured coding assistant",
+        tools=[SerenaAgnoToolkit(serena_agent)],  # type: ignore
+        # The tool calls will be shown in the UI anyway since whether to show them is configurable per tool
+        # To see detailed logs, you should use the serena logger (configure it in the project file path)
+        show_tool_calls=False,
+        markdown=True,
+        system_message=serena_agent.prompt_factory.create_system_prompt(),
+        telemetry=False,
+        memory=AgentMemory(),
+        add_history_to_messages=True,
+        num_history_responses=100,  # you might want to adjust this (expense vs. history awareness)
+    )
+
+    app = Playground(agents=[agno_agent]).get_app()
+    serve_playground_app("agno_agent:app", reload=False)
+
 
 if __name__ == "__main__":
-    serve_playground_app("agno_agent:app", reload=False)
+    main()