[Bug] Startup INFO logs (Auto-generation) cause MCP handshake timeout in VS Code (Stdio transport)

[gatspy]

When running Serena as an MCP server via stdio transport in VS Code (Copilot/Chat), the connection hangs indefinitely at Waiting for server to respond to 'initialize' request....

This issue does not occur when using claude-code CLI, but consistently fails in VS Code.

Steps to Reproduce

1. Environment: macOS, VS Code, uv installed via mise.
2. Target Project: A Go project (without an existing .serena folder or serena.toml).
3. VS Code MCP Configuration:

   "serena": {
     "type": "stdio",
     "command": "uv",
     "args": ["run", "serena", "start-mcp-server", "--context", "ide-assistant", "--project", "."]
   }

4. Launch VS Code.

Observed Behavior

VS Code shows: Waiting for server to respond to 'initialize' request... and eventually times out.

Server Logs (captured from stderr):

INFO  [MainThread] serena.config.serena_config:start:329 - Project configuration auto-generation starting ...
INFO  [MainThread] serena.config.serena_config:stop:336 - Project configuration auto-generation completed...

[opcode81]

Please provide the full Serena logs for a case where the failure occurred (~/.serena/logs).

[gatspy]

@opcode81, the following is the complete log.

INFO  2025-12-11 14:52:35,561 [MainThread] serena.cli:start_mcp_server:166 - Initializing Serena MCP server
INFO  2025-12-11 14:52:35,562 [MainThread] serena.cli:start_mcp_server:167 - Storing logs in /Users/gatspy/.serena/logs/2025-12-11/mcp_20251211-145235.txt
INFO  2025-12-11 14:52:35,565 [MainThread] serena.config.serena_config:from_config_file:406 - Loading Serena configuration from /Users/gatspy/.serena/serena_config.yml
INFO  2025-12-11 14:52:35,628 [MainThread] serena.agent:__init__:189 - Serena web dashboard started at http://127.0.0.1:24282/dashboard/index.html
INFO  2025-12-11 14:52:36,729 [MainThread] serena.agent:__init__:198 - Starting Serena server (version=0.1.4, process id=25356, parent process id=25355)
INFO  2025-12-11 14:52:36,729 [MainThread] serena.agent:__init__:199 - Configuration file: /Users/gatspy/.serena/serena_config.yml
INFO  2025-12-11 14:52:36,730 [MainThread] serena.agent:__init__:200 - Available projects: assist, assist.cloud, claude-code-change, flutter_social, guardian, parental-control, rust_beauty, rust_beauty_test_suite, ultra-zip
INFO  2025-12-11 14:52:36,730 [MainThread] serena.agent:__init__:201 - Loaded tools (36): read_file, create_text_file, list_dir, find_file, replace_regex, delete_lines, replace_lines, insert_at_line, search_for_pattern, restart_language_server, get_symbols_overview, find_symbol, find_referencing_symbols, replace_symbol_body, insert_after_symbol, insert_before_symbol, write_memory, read_memory, list_memories, delete_memory, execute_shell_command, activate_project, remove_project, switch_modes, get_current_config, check_onboarding_performed, onboarding, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, summarize_changes, prepare_for_new_conversation, initial_instructions, jet_brains_find_symbol, jet_brains_find_referencing_symbols, jet_brains_get_symbols_overview
INFO  2025-12-11 14:52:36,731 [MainThread] serena.config.serena_config:apply:108 - SerenaAgentContext[name='ide-assistant'] excluded 5 tools: create_text_file, read_file, execute_shell_command, prepare_for_new_conversation, replace_regex
INFO  2025-12-11 14:52:36,733 [MainThread] serena.agent:__init__:215 - Number of exposed tools: 19
INFO  2025-12-11 14:52:36,760 [MainThread] serena.agent:_update_active_tools:397 - Active tools (19): activate_project, check_onboarding_performed, delete_memory, find_file, find_referencing_symbols, find_symbol, get_symbols_overview, insert_after_symbol, insert_before_symbol, list_dir, list_memories, onboarding, read_memory, replace_symbol_body, search_for_pattern, think_about_collected_information, think_about_task_adherence, think_about_whether_you_are_done, write_memory
INFO  2025-12-11 14:52:36,761 [MainThread] serena.config.serena_config:start:360 - Project configuration auto-generation starting ...