[BUG] Serena MCP tools (activate_project / list_memories) extremely slow or time out

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

Calling the Serena MCP tools mcp__serena__activate_project and mcp__serena__list_memories in a
Claude Code session, both calls take an extremely long time. activate_project took more than
2 minutes and was automatically moved to a background task before eventually completing.
list_memories ran in the background and failed after exactly 240 seconds with:
"Tool execution timed out after 240 seconds."

What Should Happen?

Both tools should return within a few seconds, or at least fail fast with useful progress
feedback, instead of silently hanging for minutes — especially on a directory that is not a
typical source-code project (mostly JSON/TSV/Markdown data files, no language server needed).

Error Messages/Logs

mcp__serena__activate_project on /home/c3phur/.exegol/workspaces
-> still running after 121s, moved to background task kfb833nqp
-> eventually completed with:
Created and activated a new project with name 'workspaces' at /home/c3phur/.exegol/workspaces.
Active language servers: .
File encoding: utf-8.
Onboarding has not been performed yet.

mcp__serena__list_memories (background task kh98x9m22)
-> failed: Error executing tool list_memories: Tool execution timed out after 240 seconds.

Steps to Reproduce

1. Open a Claude Code session with the Serena MCP server configured, working directory set to

a git repo that is data-heavy rather than a typical source-code project (in my case: ~90
subfolders of JSON/TSV/Markdown files tracking bug-bounty programs, no language project
structure at all).

1. Call mcp__serena__activate_project with that directory as project.
2. Observe the call run well past 2 minutes and get automatically moved to a background task.
3. Immediately after, call mcp__serena__list_memories.
4. Observe it fail after 240 seconds with "Tool execution timed out after 240 seconds."

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.276 (Claude Code)

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

Working directory is a bug-bounty program tracking workspace (git repo), ~90 subfolders each
holding some_useful_files.json + markdown triage reports — not a software project. This
may explain why Serena's project indexing is unusually slow here. The calls were triggered
indirectly via the SuperClaude framework's /sc:save command, which defaults to Serena MCP for
session persistence.