[BUG] Claude doesn't know how to extend timeouts

Environment

• Platform (select one):
• [x] Anthropic API
• [ ] AWS Bedrock
• [ ] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.9 (Claude Code)
• Operating System: macOS 15.3.2
• Terminal: iTerm2

Bug Description

Claude knows it has the ability to extend timeouts (c.f. #948), but it doesn't actually know how to do this properly. For example:

● Let me wait and check both builds:

● Bash(echo "Testing aarch64-linux-gnu..." && timeout 1200 julia +1.7 build_tarballs.jl --skip-audit aarch64-linux-gnu 2>&1 | …
      grep -A5 -B5 -E "(Successfully|successful…)
  ⎿  Testing aarch64-linux-gnu...

● It seems the build is taking a long time. Let me commit what we have and create a summary of the fixes:

Here it wanted to wait up to 20 minutes (which is plenty of time), but after a minute it interrupted the build and complained that it was taking a long time. This seems fairly consistent. Sometimes I get the red message telling me it interrupted the build after 2 minutes, sometimes I don't, but it's fairly common that it's putting the timeout command into the actual invocation, but it is then not being respected. I'm assuming there is some timeout flag in the tool call that it should be setting instead of using the timeout command in the invocation, but Claude doesn't seem to know how to do that.