Project-scoped MCP connectors fail to attach in interactive sessions (100% reproducible across 15 projects), while global-scope connectors and scheduled tasks work fine

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?

Project-scoped MCP connectors (defined under projects.<path>.mcpServers in .claude.json) do not attach in interactive chat sessions, even when the configuration is verified correct. This is 100% reproducible — tested across 15 separate client projects, one at a time, in isolation. The same connectors work reliably in two other contexts: they attach correctly when invoked via a scheduled task bound to the same project folder, and global-scope connectors (top-level mcpServers, not under any project) always attach in every session. No error appears — the connector's tools simply never show up as available.

Possibly related (not duplicates): #88758 (Desktop app doesn't connect project-scoped .mcp.json HTTP servers — same symptom class, different platform/transport) and #88800 (background session launch silently disables project connectors — checked our own .claude/settings.local.json files for this exact pattern, not present, but same general bug family).

What Should Happen?

The project's configured connector tools should be available in the session, the same way they are in a scheduled task run bound to that project.

Error Messages/Logs

None — this is the notable part. No error, no timeout, no pending-approval state. The connector's tools are simply absent from the available tool list, with nothing logged to indicate why.

Steps to Reproduce

Configure a project-scoped MCP stdio connector under projects.<absolute-path>.mcpServers in .claude.json, pointing to a working external service (verified reachable independently of MCP).
Open a fresh interactive chat with that project as the working directory (or switch an existing session's working directory to it).
Search for the connector's tools — they never appear.

Ruled out: config errors (credentials verified working via direct API calls), a pending-approval dialog (checked the app UI directly), app restart, full OS reboot, concurrent-session load (fails even one project at a time in isolation), and the disabledMcpjsonServers poisoning described in #88800 (checked directly across 16 project folders, not present).

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.226

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_