[BUG] In 2.1.92 MCP tool names with "__" in them cause issues

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?

We use "__" as a separator in our tool names. After updating to 2.1.92, things broke. I validated rolling back to 2.1.91 things were preserved, and after changing our separator to something else, 2.1.92 works great as well.

What Should Happen?

Not fail using my tool because I chose to use "__" as a separator. Or at least alert me to the fact that I can't use that.

Error Messages/Logs

Found it. Claude Code was updated today from 2.1.91 to 2.1.92:

  2.1.90  (Apr 1)
  2.1.91  (Apr 3)  ← worked
  2.1.92  (Apr 6)  ← broke today, symlinked at 10:24

  So yes, this is almost certainly a change in Claude Code 2.1.92 that rejects or filters MCP tool names containing __ (double underscore), since that's Claude Code's own internal mcp__<server>__<tool> delimiter.

  Your options:

  1. Report as a Claude Code bug — tool names containing __ should be valid MCP tool names. File at https://github.com/anthropics/claude-code/issues
  2. Workaround now — change tool_separator from "__" to "_" in config.toml and restart. This avoids the conflict while keeping the prefix feature
  3. Verify by downgrading — you could switch back to 2.1.91 to confirm the regression: ln -sf /u/mpalmer/.local/share/claude/versions/2.1.91 /u/mpalmer/.local/bin/claude

  I'd suggest doing both #1 and #2 — report the bug and change the separator as a practical fix. Want me to proceed with changing the separator?

Steps to Reproduce

1. Create a tool with "__" in the name
2. Profit

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.91

Claude Code Version

2.1.92

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Windows Terminal

Additional Information

_No response_