[BUG] The global configuration for autoUpdates is not applied.

Environment

• Platform (select one):
• [ ] Anthropic API
• [ ] AWS Bedrock
• [x] Google Vertex AI
• [ ] Other: <!-- specify -->
• Claude CLI version: 1.0.38
• Operating System: macOS 15.5
• Terminal: vscode terminal

Bug Description

According to the Claude Code settings, I set autoUpdates to false with the command below and confirmed that it was indeed set to false:

claude config set -g autoUpdates false
claude config list -g
>>>  "autoUpdates": "false"

However, when I launch Claude Code with the env CLAUDE_CONFIG_DIR=$HOME/.claude claude command, it still performs an automatic update and switches to version 1.0.41.

I also tried disabling automatic updates by setting the environment variable DISABLE_AUTOUPDATER=1, but the update still runs.

Also, I have the command env CLAUDE_CONFIG_DIR=$HOME/.claude claude set up as an alias in my .zshrc, but whenever I start the claude command, that alias gets deleted. This is a serious bug.

Steps to Reproduce

1. npm install -g @anthropic-ai/claude-code@1.0.38
2. claude config set -g autoUpdates false
3. env CLAUDE_CONFIG_DIR=$HOME/.claude claude

Expected Behavior

<!-- What you expected to happen -->
Auto updates do not run.
Alias in my .zshrc is not deleted.

Actual Behavior

Auto updates run and switches to version 1.0.41.
Alias in my .zshrc is deleted.