[BUG] Compacting throws an error

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?

Bug: /compact command fails with "Tool names must be unique" error

Description

The /compact slash command fails with an API error indicating duplicate tool names, despite having a minimal MCP server configuration.

Environment

• Claude Code version: 2.0.70
• Model: Opus 4.5 (claude-opus-4-5-20251101)
• OS: macOS (Darwin 25.1.0)
• Platform: darwin
• Node.js: 24.4.1+ (local)

Steps to Reproduce

1. Start a Claude Code session in a project with MCP server configurations
2. Have a conversation (even a simple greeting)
3. Run /compact

Expected Behavior

Conversation should be compacted/summarized to reduce context usage.

Actual Behavior

Error: Error during compaction: Error: API Error: 400
{
"type": "error",
"error": {
"type": "invalid_request_error",
"message": "tools: Tool names must be unique."
},
"request_id": "req_011CWAdUXuj1K2ddgLpmxhmf"
}

Verified MCP Configuration

Project .mcp.json:
{
"mcpServers": {
"Neon": {
"command": "npx",
"args": ["-y", "mcp-remote", "https://mcp.neon.tech/mcp"]
}
}
}

Project .claude/settings.local.json:
{
"enableAllProjectMcpServers": false,
"enabledMcpjsonServers": ["Neon"]
}

User-level project config (~/.claude.json entry for this project):
{
"mcpServers": {
"figma-desktop": {
"type": "http",
"url": "http://127.0.0.1:3845/mcp"
}
},
"disabledMcpServers": []
}

Global ~/.claude.json:
{
"mcpServers": {}
}

MCP Tools in Permissions Allow List

Only Neon tools are in the permissions:

• mcp__Neon__describe_table_schema
• mcp__Neon__get_database_tables
• mcp__Neon__list_projects
• mcp__Neon__run_sql
• mcp__Neon__run_sql_transaction

Hooks Configuration

{
"hooks": {
"PreCompact": [{
"hooks": [{
"type": "command",
"command": "bash ~/.claude/hooks/pre-compact.sh"
}]
}],
"PreToolUse": [...],
"PostToolUse": [...],
"Notification": [...],
"Stop": [...],
"SubagentStop": [...]
}
}

Analysis

The error occurs despite:

1. Only 2 MCP servers configured (Neon + figma-desktop)
2. These servers have completely different tool namespaces
3. No duplicate tool names in the permissions list
4. disabledMcpServers is empty

This suggests the bug is internal to Claude Code's compact operation rather than a user configuration issue. Possible causes:

• Built-in tools being registered with duplicates during compaction
• Tool deduplication logic failing
• Some tools being registered multiple times during the compact API call construction

What Should Happen?

It should compact with no error being thrown.

Error Messages/Logs

> /compact
  ⎿  Error: Error during compaction: Error: API Error: 400 {"type":"error","error":{"type":"invalid_request_error","message":"tools: Tool names must be unique."},"request_id":"req_011CWAdzsCBFgCkCnd2n4N6D"}

Steps to Reproduce

start Claude
type "hi"
/compact

getting the error.

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Claude code .68

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_