[BUG] Tool calls stall for 10-20 minutes after text output on v2.1.89 + Bun GC crash

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?

Text output appears but tool calls stall for 10-20 minutes, especially after file edits. Had a Bun GC crash earlier with following context:

Exception: EXC_BREAKPOINT / SIGTRAP
Faulting thread: Heap Helper Thread (JavaScriptCore GC)
Process ran ~42 min before crash
Termination: Trace/BPT trap: 5

Started after the time of the crash (March 31), with it struggling to find context within an existing project. Eventually it did recover, but tool calls including sub-agents becoming unresponsive or reporting internal errors and having to repeatedly restart the asks

Fresh sessions still slow, within token limits, no zombie processes

Conversational sessions with no tool use remain responsive. Stalling occurs in sessions with heavy tool use (file edits, reads, searches). Context payload may be a factor in longer sessions.

What Should Happen?

Tool calls should execute immediately after text output, not stall for minutes. Simple single-line edits should complete in seconds.

Error Messages/Logs

Steps to Reproduce

1. Start a Claude Code session on Opus 4.6
2. Work on a multi-file editing task over an extended session (~30-40 min)
3. After a file edit completes, observe that Claude outputs text describing the next action but the subsequent tool

call stalls for 5-10 minutes

1. Issue persists across fresh sessions

Claude Model

Opus

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.89

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

2.1.89-2026-03-31-201151.ips.zip