Initialize stderr stream logger early

and make the fastmcp configuration function do nothing if log handlers already exist

src/serena/cli.py

@@ -16,6 +16,7 @@ from serena.config.serena_config import ProjectConfig, SerenaConfig
 from serena.constants import (
     DEFAULT_CONTEXT,
     DEFAULT_MODES,
+    SERENA_LOG_FORMAT,
     SERENA_MANAGED_DIR_IN_HOME,
     SERENAS_OWN_CONTEXT_YAMLS_DIR,
     SERENAS_OWN_MODE_YAMLS_DIR,
@@ -138,11 +139,17 @@ class TopLevelCommands(AutoRegisteringGroup):
         tool_timeout: float | None,
     ) -> None:
         # initialize logging, using INFO level initially (will later be adjusted by SerenaAgent according to the config)
+        #   * memory log handler (for use by GUI/Dashboard)
+        #   * stream handler for stderr (for direct console output, which will also be captured by clients like Claude Desktop)
+        # (Note that stdout must never be used for logging, as it is used by the MCP server to communicate with the client.)
         Logger.root.setLevel(logging.INFO)
         memory_log_handler = MemoryLogHandler()
         Logger.root.addHandler(memory_log_handler)
+        stderr_handler = logging.StreamHandler(stream=sys.stderr)
+        stderr_handler.formatter = logging.Formatter(SERENA_LOG_FORMAT)
+        Logger.root.addHandler(stderr_handler)
 
-        log.info("Starting Serena MCP server")
+        log.info("Initializing Serena MCP server")
         project_file = project_file_arg or project
         factory = SerenaMCPFactorySingleProcess(context=context, project=project_file, memory_log_handler=memory_log_handler)
         server = factory.create_mcp_server(

src/serena/mcp.py

@@ -7,7 +7,6 @@ from abc import abstractmethod
 from collections.abc import AsyncIterator, Iterator, Sequence
 from contextlib import asynccontextmanager
 from dataclasses import dataclass
-from logging import Formatter, Logger, StreamHandler
 from typing import Any, Literal, cast
 
 import docstring_parser
@@ -22,22 +21,19 @@ from serena.agent import (
     SerenaConfig,
 )
 from serena.config.context_mode import SerenaAgentContext, SerenaAgentMode
-from serena.constants import DEFAULT_CONTEXT, DEFAULT_MODES
+from serena.constants import DEFAULT_CONTEXT, DEFAULT_MODES, SERENA_LOG_FORMAT
 from serena.tools import Tool
 from serena.util.exception import show_fatal_exception_safe
 from serena.util.logging import MemoryLogHandler
 
 log = logging.getLogger(__name__)
-LOG_FORMAT = "%(levelname)-5s %(asctime)-15s %(name)s:%(funcName)s:%(lineno)d - %(message)s"
-LOG_LEVEL = logging.INFO
 
 
 def configure_logging(*args, **kwargs) -> None:  # type: ignore
-    # configure logging to stderr (will be captured by Claude Desktop); stdio is the MCP communication stream and cannot be used!
-    Logger.root.setLevel(LOG_LEVEL)
-    handler = StreamHandler(stream=sys.stderr)
-    handler.formatter = Formatter(LOG_FORMAT)
-    Logger.root.addHandler(handler)
+    # We only do something here if logging has not yet been configured.
+    # Normally, logging is configured in the MCP server startup script.
+    if not logging.is_enabled():
+        logging.basicConfig(level=logging.INFO, stream=sys.stderr, format=SERENA_LOG_FORMAT)
 
 
 # patch the logging configuration function in fastmcp, because it's hard-coded and broken